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- PDB-5k09: Crystal Structure of COMT in complex with a thiazole ligand -

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Basic information

Entry
Database: PDB / ID: 5k09
TitleCrystal Structure of COMT in complex with a thiazole ligand
ComponentsCatechol O-methyltransferase
KeywordsTRANSFERASE / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION / CATECHOL
Function / homology
Function and homology information


Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / positive regulation of homocysteine metabolic process / Methylation / norepinephrine secretion / response to dopamine / mastication / catechol-containing compound metabolic process / catecholamine catabolic process / catechol O-methyltransferase activity ...Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / positive regulation of homocysteine metabolic process / Methylation / norepinephrine secretion / response to dopamine / mastication / catechol-containing compound metabolic process / catecholamine catabolic process / catechol O-methyltransferase activity / renal sodium excretion / : / : / S-adenosylhomocysteine metabolic process / catechol O-methyltransferase / renal filtration / developmental process / renin secretion into blood stream / dopamine secretion / negative regulation of dopamine metabolic process / renal albumin absorption / catecholamine metabolic process / habituation / artery development / response to salt / short-term memory / S-adenosylmethionine metabolic process / cerebellar cortex morphogenesis / dopamine catabolic process / norepinephrine metabolic process / cellular response to phosphate starvation / glomerulus development / fear response / multicellular organismal reproductive process / synaptic transmission, dopaminergic / response to angiotensin / cellular response to cocaine / estrogen metabolic process / exploration behavior / response to food / cholesterol efflux / response to temperature stimulus / response to pain / response to corticosterone / prostaglandin metabolic process / glycogen metabolic process / dopamine metabolic process / startle response / detection of temperature stimulus involved in sensory perception of pain / : / behavioral fear response / multicellular organismal response to stress / response to amphetamine / : / learning / response to cytokine / kidney development / female pregnancy / negative regulation of smooth muscle cell proliferation / visual learning / multicellular organism growth / response to organic cyclic compound / response to toxic substance / memory / cognition / regulation of blood pressure / response to wounding / response to estrogen / gene expression / cell body / postsynapse / methylation / postsynaptic membrane / vesicle / response to oxidative stress / response to lipopolysaccharide / dendritic spine / learning or memory / response to hypoxia / response to xenobiotic stimulus / axon / glutamatergic synapse / dendrite / magnesium ion binding / membrane / cytosol
Similarity search - Function
Catechol O-methyltransferase, eukaryotic / O-methyltransferase / Class I-like SAM-dependent O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6PQ / : / PHOSPHATE ION / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsEhler, A. / Rodriguez-Sarmiento, R.M. / Rudolph, M.G.
CitationJournal: J. Med. Chem. / Year: 2016
Title: Design of Potent and Druglike Nonphenolic Inhibitors for Catechol O-Methyltransferase Derived from a Fragment Screening Approach Targeting the S-Adenosyl-l-methionine Pocket.
Authors: Lerner, C. / Jakob-Roetne, R. / Buettelmann, B. / Ehler, A. / Rudolph, M. / Rodriguez Sarmiento, R.M.
History
DepositionMay 17, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Dec 21, 2016Group: Database references
Revision 1.3Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.4May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catechol O-methyltransferase
B: Catechol O-methyltransferase
C: Catechol O-methyltransferase
D: Catechol O-methyltransferase
E: Catechol O-methyltransferase
F: Catechol O-methyltransferase
G: Catechol O-methyltransferase
H: Catechol O-methyltransferase
I: Catechol O-methyltransferase
J: Catechol O-methyltransferase
K: Catechol O-methyltransferase
L: Catechol O-methyltransferase
M: Catechol O-methyltransferase
N: Catechol O-methyltransferase
O: Catechol O-methyltransferase
P: Catechol O-methyltransferase
Q: Catechol O-methyltransferase
R: Catechol O-methyltransferase
S: Catechol O-methyltransferase
T: Catechol O-methyltransferase
U: Catechol O-methyltransferase
V: Catechol O-methyltransferase
W: Catechol O-methyltransferase
X: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)592,585118
Polymers581,99324
Non-polymers10,59394
Water9,638535
1
A: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6665
Polymers24,2501
Non-polymers4174
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6274
Polymers24,2501
Non-polymers3783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7225
Polymers24,2501
Non-polymers4734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7225
Polymers24,2501
Non-polymers4734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6274
Polymers24,2501
Non-polymers3783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6274
Polymers24,2501
Non-polymers3783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6665
Polymers24,2501
Non-polymers4174
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7225
Polymers24,2501
Non-polymers4734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7225
Polymers24,2501
Non-polymers4734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6665
Polymers24,2501
Non-polymers4174
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7616
Polymers24,2501
Non-polymers5125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6665
Polymers24,2501
Non-polymers4174
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
M: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7616
Polymers24,2501
Non-polymers5125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
N: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7616
Polymers24,2501
Non-polymers5125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
O: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6665
Polymers24,2501
Non-polymers4174
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
16
P: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6274
Polymers24,2501
Non-polymers3783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
17
Q: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7225
Polymers24,2501
Non-polymers4734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
18
R: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6665
Polymers24,2501
Non-polymers4174
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
19
S: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7616
Polymers24,2501
Non-polymers5125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
20
T: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7225
Polymers24,2501
Non-polymers4734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
21
U: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6274
Polymers24,2501
Non-polymers3783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
22
V: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7225
Polymers24,2501
Non-polymers4734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
23
W: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7225
Polymers24,2501
Non-polymers4734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
24
X: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6274
Polymers24,2501
Non-polymers3783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.035, 138.418, 158.501
Angle α, β, γ (deg.)91.480, 97.190, 90.160
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ...
Catechol O-methyltransferase


Mass: 24249.695 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Comt / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22734, catechol O-methyltransferase
#2: Chemical...
ChemComp-6PQ / 5-{3-[(4-methoxyphenyl)methyl]-1H-pyrazol-5-yl}-2,4-dimethyl-1,3-thiazole


Mass: 299.391 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C16H17N3OS
#3: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 58 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 535 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M TRIS-HCL pH 7, 1.8 M ammonium sulfate, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 2.7→48.84 Å / Num. obs: 190265 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 1.69 % / Biso Wilson estimate: 55.024 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.98
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.7-2.770.8391.02194.7
2.77-2.850.6341.36195.1
2.85-2.930.5151.73195.6
2.93-3.020.4292.04195.8
3.02-3.120.3352.61195.9
3.12-3.230.2593.42195.8
3.23-3.350.1984.32195.9
3.35-3.490.1386.03195.9
3.49-3.640.1057.55196.1
3.64-3.820.0888.79195.7
3.82-4.020.07110.3195.9
4.02-4.270.05112.73195.7
4.27-4.560.04115.22195.2
4.56-4.930.03716.84196.6
4.93-5.40.04115.43196.6
5.4-6.040.04514.08196.1
6.04-6.970.03815.76196.8
6.97-8.540.02820.59195.8
8.54-12.070.0228.56194.5
12.070.02328.64192.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
PHENIXrefinement
XDSdata reduction
PHENIXphasing
RefinementResolution: 2.7→48.836 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.52
RfactorNum. reflection% reflection
Rfree0.2356 9568 5.03 %
Rwork0.1647 --
obs0.1683 190265 97.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 178.62 Å2 / Biso mean: 55.3101 Å2 / Biso min: 11.95 Å2
Refinement stepCycle: final / Resolution: 2.7→48.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40482 0 622 535 41639
Biso mean--50.59 41.59 -
Num. residues----5174
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.52451.2749-0.35411.7199-0.58484.39420.0542-0.0687-0.38010.12160.0380.06710.5057-0.3888-0.08760.49-0.0573-0.03210.3761-0.06570.4341-21.950231.0272-35.016
22.05390.37760.77911.45630.40692.41250.02470.0882-0.1805-0.10370.00830.0952-0.1194-0.1828-0.0070.32670.0008-0.01720.2983-0.03160.3314-15.382347.4992-36.4101
31.50780.5123-0.12661.37750.37172.45320.05420.00250.03580.0315-0.14220.1024-0.6136-0.00880.12910.4318-0.0144-0.02510.2549-0.01020.3045-13.777957.9582-23.3721
42.31590.88240.42952.2284-0.48334.4695-0.1327-0.4051-0.5813-0.30020.50460.17680.8475-0.4348-0.19210.484-0.0968-0.00340.2216-0.02340.4746-13.7244-39.94481.8296
51.66010.09050.29351.94670.61622.1705-0.026-0.0766-0.0891-0.19240.08320.13240.0429-0.145-0.0540.3355-0.06650.02470.24450.07090.2917-7.3156-23.75561.207
61.0031-0.0457-0.10990.87570.6572.0224-0.1447-0.23130.1176-0.06360.1192-0.1664-0.14710.19670.02450.3486-0.0510.03390.29620.07310.2991-1.7367-14.905113.1014
71.53581.5068-0.07992.8026-2.34962.9664-0.0138-0.04610.02910.1453-0.0407-0.0733-0.1454-0.0798-0.01610.4028-0.01990.07870.17960.03070.4159-11.559-16.633418.961
84.219-1.30310.76173.4594-1.3434.1631-0.1089-0.39790.82980.4146-0.2083-1.0391-0.36090.67380.30460.4087-0.1197-0.04540.7608-0.00120.564629.563341.3733-3.7384
95.3945-1.5388-2.37952.1450.34873.8309-0.0779-0.9144-0.83820.60710.06530.1077-0.13370.31270.07660.4083-0.00620.03030.76990.11240.564525.524730.7024-3.0326
103.1867-0.01950.26873.33690.59583.3623-0.1445-0.4369-0.00680.45320.3298-0.10310.4110.2366-0.1040.30510.0194-0.02410.39810.04690.47213.470829.82-8.8143
112.6180.50310.45670.535-0.45781.76780.07750.18770.0426-0.1407-0.0695-0.2560.0070.58810.00340.36780.03150.01950.4934-0.01710.464819.802835.3813-21.1172
124.0929-0.7209-1.36513.87250.95845.5088-0.24750.13730.4688-0.79180.52060.0845-0.89340.0782-0.01540.43180.0378-0.03530.3750.13290.41434.724941.6176-25.1826
131.06170.2058-0.29960.49-0.26541.83260.01880.28890.0083-0.1058-0.07770.10840.10050.03140.01030.3550.0487-0.00380.2991-0.02530.38461.682234.4217-21.2754
141.2253-0.3064-0.20521.6482-0.19263.93010.1994-0.1902-0.47660.0722-0.14940.21080.5759-0.39040.05610.3909-0.0107-0.03880.40480.02360.47821.066929.3277-10.9581
151.1315-0.4038-1.47121.15150.86845.2439-0.03630.1712-0.146-0.1372-0.07270.0117-0.4672-0.04930.22380.3066-0.02640.02560.30510.05950.40160.450430.7972-15.462
163.0563-0.2121.02920.4953-0.14451.57040.13790.3931-0.1142-0.215-0.13950.2609-0.091-0.1875-0.01250.35060.0376-0.010.55320.03350.4702-34.333534.2853-11.7634
172.2507-0.59750.05920.8041-0.07931.8710.0747-0.1058-0.34050.1630.16530.157-0.0426-0.3471-0.19750.34530.01150.02010.55150.06080.4384-34.707130.18911.7331
184.3812-0.23231.40375.4110.28543.51690.0009-1.0716-0.01070.0250.0330.6445-0.37050.08410.07160.34270.04080.03390.3904-0.0150.3685-20.087434.22784.4031
191.21010.5454-0.40940.8635-1.00791.68250.0478-0.2874-0.03440.12840.18440.1131-0.1036-0.047-0.17240.3878-0.0757-0.00320.36830.09340.4404-14.916629.58280.7838
200.82670.4973-0.63371.8957-1.38332.7791-0.0252-0.0203-0.1063-0.17280.18470.09470.2913-0.12-0.07440.32810.028-0.00310.3075-0.01330.4152-14.039929.3653-8.5516
212.3753-1.0066-1.27373.3341-1.23972.36380.0871-0.2960.5830.1458-0.80880.1147-0.58120.43190.14121.2220.1893-0.3240.6111-0.35770.8034-6.615676.415918.4457
220.69250.3883-0.06591.610.38781.588-0.3779-0.2750.5315-0.013-0.0684-0.2142-1.0037-0.35440.3261.07940.1591-0.08060.4297-0.09470.5748-15.892472.12986.9317
231.0131-0.2090.26672.5387-0.44041.2025-0.349-0.82390.55930.32640.20240.1452-0.8281-0.55090.07520.94190.2172-0.02440.757-0.24660.6341-19.686970.046715.7929
240.9122-0.29780.79391.269-0.05840.896-0.196-0.92350.36970.30050.19820.0155-0.2769-0.91530.04910.87690.23480.03641.0012-0.1940.5601-27.517961.706518.6009
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1131.13180.6027-0.00391.4879-0.18591.91430.1410.35110.185-0.1799-0.00210.1582-0.47320.2338-0.11870.49720.033-0.04150.49950.02970.3337-27.3976-19.3171-71.7315
1143.21220.74640.38020.14980.43771.50630.18420.4763-0.1454-0.1594-0.04020.13230.0369-0.232-0.09830.34930.0557-0.04270.5745-0.07950.4849-45.8417-36.171-52.693
1153.0656-0.52740.67670.76520.32561.81240.0475-0.4236-0.22370.1670.05250.2499-0.0203-0.6132-0.05830.3164-0.00630.03270.49680.01770.454-45.0306-34.0661-39.0537
1166.19841.0338-2.3816.4625-1.3717.512-0.5187-0.42160.65270.63920.3715-0.2354-1.5117-0.90160.12180.3360.0222-0.09740.3965-0.06370.3913-29.4061-28.2574-35.2314
1171.71890.19070.151.0251-0.94031.640.20720.0412-0.22810.10780.01860.00720.00580.228-0.17330.29930.02-0.01490.2337-0.03230.3331-26.0213-37.3288-43.3741
1181.47951.21610.10476.18071.11611.3369-0.41490.06030.2746-1.13530.28430.8951-0.3914-0.73090.05210.8309-0.0196-0.20190.96740.10570.69434.820862.213337.0557
1192.1047-0.1658-1.26291.1606-0.68462.5206-0.2824-0.15950.26610.896-0.2549-0.4538-1.0755-0.35340.23041.26390.0115-0.27260.55650.05660.815841.044468.730744.2737
1202.72730.38550.89531.5067-0.46891.9068-0.50490.06810.77920.02140.1562-0.0821-0.49920.12130.27030.6882-0.0024-0.11720.3762-0.04630.723147.502661.237453.2939
1211.2047-0.36690.87711.64290.01571.313-0.27340.86910.5867-0.4450.0331-0.1849-0.41620.54580.15720.6203-0.1966-0.03640.84770.2280.566151.499657.60940.7001
1222.88230.3948-0.29111.21370.30723.40910.19662.2490.493-0.4158-0.1652-0.45230.23520.85260.05810.682-0.00280.11611.27060.05730.548960.884445.249740.0364
1234.8024-0.35681.06563.7367-0.59682.942-0.08510.70780.2448-0.3338-0.37980.09370.27940.37110.31860.4866-0.0710.03850.5783-0.05010.42453.393443.829950.85
1240.1813-0.3340.21960.80.12260.9114-0.23240.07480.02570.0050.1286-0.3428-0.07980.62040.05080.3826-0.10370.05240.57720.0470.475656.047948.908554.927
1254.1426-1.2677-0.3392.4161-0.2231.3359-0.4951-0.33540.51610.06340.2672-0.5455-0.1174-0.05270.15580.36530.0273-0.07760.5182-0.06850.442953.756548.797362.8965
1264.08060.4346-0.67811.0822-0.27592.3708-0.1655-0.091-0.136-0.110.195-0.3251-0.35550.57160.04480.32080.0076-0.04620.5426-0.14510.496652.771451.675262.3363
1271.94330.1772-0.97832.78821.32362.1392-0.19840.09720.3421-0.3040.2004-0.3135-0.37070.46470.02290.5914-0.0644-0.12240.3325-0.03830.576336.490975.356669.0273
1281.28980.0478-0.09321.3710.25111.2122-0.26530.16060.617-0.1883-0.0321-0.1372-0.2322-0.09720.22380.42680.065-0.11780.4775-0.07560.577725.293863.982465.1354
1290.02030.2492-0.17991.6298-0.42141.6796-0.2381-0.39370.35950.0661-0.0510.2362-0.4426-0.47030.23510.47680.1322-0.12020.4535-0.19980.606624.409869.851773.3588
1301.37950.61680.03712.0414-0.42071.2246-0.2343-0.23820.33970.5324-0.25480.6053-0.4255-0.67520.39390.51930.1256-0.00830.6419-0.25160.646216.490763.339580.5349
1314.48680.93360.10822.38350.52411.5893-0.298-0.64520.45890.29310.10680.00340.4384-0.01550.1370.54480.0904-0.04680.4569-0.16710.402821.525351.754474.3567
1322.1383-0.394-0.20081.02720.61141.285-0.13470.20910.05780.1058-0.03060.2422-0.0872-0.27540.11470.3560.0568-0.08120.4854-0.12620.483520.153550.386664.4906
1335.6247-0.8429-1.62491.80030.55862.03930.0836-0.4634-0.4295-0.2282-0.18010.2306-0.0751-0.10030.14420.422-0.0635-0.06950.5367-0.12420.485322.128850.857760.509
1341.71140.5463-1.37055.09150.87961.5031-0.4728-0.1540.0745-0.4541-0.17070.5047-0.5737-0.02660.48281.0052-0.0183-0.27970.35640.13330.6036-6.876384.3618-17.3317
1353.90650.1263-2.4792.9481-0.22754.4001-0.26360.07270.18760.6663-0.1237-0.2623-0.7533-0.19070.34411.12270.0308-0.1910.35270.03190.6392-4.528882.4604-8.4891
1362.3289-0.55670.75752.0405-0.65031.5706-0.3429-0.53930.48820.4294-0.03280.0769-0.2625-0.09020.32310.83010.013-0.09250.306-0.04380.59733.422773.3284-5.4868
1371.56640.0060.37771.3910.56691.4825-0.22280.31850.7139-0.10550.0192-0.2937-0.55220.22210.140.8859-0.1625-0.11220.37140.13650.68619.357874.97-15.1713
1380.6668-1.1111-0.7145.02893.36433.426-0.24980.4770.5291-0.1478-0.2937-0.3373-0.49640.00030.48191.2305-0.0598-0.16760.44550.09310.52350.865380.2108-22.089
1391.2493-0.53850.62221.00840.07410.67130.03190.51350.3822-0.3428-0.3249-0.3756-0.10340.41790.25080.7947-0.1238-0.05720.52370.15140.605712.590769.5338-22.0179
1403.1431-0.90280.69023.19850.13772.13160.47251.0964-0.3514-0.2953-0.4015-0.0168-0.076-0.12180.02120.7208-0.1040.05370.27220.04540.50610.612256.721-17.9854
1413.72640.2777-1.01041.0427-0.23561.40570.42340.1738-0.03310.2839-0.2611-0.32140.0040.1545-0.1290.5043-0.1037-0.09190.32240.06990.518312.039561.8613-10.6028
1424.2872-2.1118-1.13881.846-0.40342.42320.4057-0.1206-0.12420.1345-0.4837-0.5801-0.12970.59870.04650.5369-0.16580.01060.23530.05730.543112.64152.7101-7.9533
1435.7586-1.5695-2.82111.61470.8282.4362-0.3562-0.29730.39430.55570.301-0.4874-0.09310.1585-0.04130.67430.0042-0.13390.37870.04680.41496.905862.1474-0.1111
1444.75821.0659-1.58631.3699-0.47382.2992-0.0490.3790.23480.43620.1924-0.2751-0.05040.0523-0.08460.6610.0394-0.04120.27950.01080.42448.645660.4354-3.0151
1450.7977-0.8088-0.17341.5324-0.74681.1095-0.07551.52210.9103-0.054-0.2741-0.0694-0.36-0.1095-0.00940.7836-0.0285-0.08410.7120.50960.8082-13.35195.5025-69.9167
1462.16930.29880.10322.4922-0.28520.60390.21012.29521.0589-0.6550.0027-0.0052-0.06890.6692-0.00180.86070.02450.08781.06510.67990.6174-1.7554-0.7044-72.1647
1470.905-0.30570.98520.4247-0.55081.33780.34492.1340.4994-0.8393-0.3946-0.15240.04660.33720.15690.9420.21750.09311.90870.66050.1808-0.9884-4.9433-79.2508
1481.3351-0.33870.20261.384-0.40771.51490.31260.51150.0131-0.2228-0.3066-0.08190.13530.5738-0.00460.5497-0.02310.04550.49810.13030.3883-0.3181-14.202-63.3349
1493.8264-0.3867-1.2571.2881-0.51872.471-0.15770.28040.28270.34510.0733-0.3813-0.28180.00270.01410.5563-0.0226-0.10420.33980.10180.4033-3.4412-7.629-54.2915
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 35 )A2 - 35
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 143 )A36 - 143
3X-RAY DIFFRACTION3chain 'A' and (resid 144 through 218 )A144 - 218
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 35 )B2 - 35
5X-RAY DIFFRACTION5chain 'B' and (resid 36 through 136 )B36 - 136
6X-RAY DIFFRACTION6chain 'B' and (resid 137 through 188 )B137 - 188
7X-RAY DIFFRACTION7chain 'B' and (resid 189 through 216 )B189 - 216
8X-RAY DIFFRACTION8chain 'C' and (resid 2 through 16 )C2 - 16
9X-RAY DIFFRACTION9chain 'C' and (resid 17 through 35 )C17 - 35
10X-RAY DIFFRACTION10chain 'C' and (resid 36 through 57 )C36 - 57
11X-RAY DIFFRACTION11chain 'C' and (resid 58 through 143 )C58 - 143
12X-RAY DIFFRACTION12chain 'C' and (resid 144 through 156 )C144 - 156
13X-RAY DIFFRACTION13chain 'C' and (resid 157 through 188 )C157 - 188
14X-RAY DIFFRACTION14chain 'C' and (resid 189 through 199 )C189 - 199
15X-RAY DIFFRACTION15chain 'C' and (resid 200 through 217 )C200 - 217
16X-RAY DIFFRACTION16chain 'D' and (resid 2 through 70 )D2 - 70
17X-RAY DIFFRACTION17chain 'D' and (resid 71 through 136 )D71 - 136
18X-RAY DIFFRACTION18chain 'D' and (resid 137 through 156 )D137 - 156
19X-RAY DIFFRACTION19chain 'D' and (resid 157 through 188 )D157 - 188
20X-RAY DIFFRACTION20chain 'D' and (resid 189 through 216 )D189 - 216
21X-RAY DIFFRACTION21chain 'E' and (resid 2 through 21 )E2 - 21
22X-RAY DIFFRACTION22chain 'E' and (resid 22 through 70 )E22 - 70
23X-RAY DIFFRACTION23chain 'E' and (resid 71 through 105 )E71 - 105
24X-RAY DIFFRACTION24chain 'E' and (resid 106 through 136 )E106 - 136
25X-RAY DIFFRACTION25chain 'E' and (resid 137 through 188 )E137 - 188
26X-RAY DIFFRACTION26chain 'E' and (resid 189 through 216 )E189 - 216
27X-RAY DIFFRACTION27chain 'F' and (resid 2 through 16 )F2 - 16
28X-RAY DIFFRACTION28chain 'F' and (resid 17 through 35 )F17 - 35
29X-RAY DIFFRACTION29chain 'F' and (resid 36 through 57 )F36 - 57
30X-RAY DIFFRACTION30chain 'F' and (resid 58 through 70 )F58 - 70
31X-RAY DIFFRACTION31chain 'F' and (resid 71 through 92 )F71 - 92
32X-RAY DIFFRACTION32chain 'F' and (resid 93 through 129 )F93 - 129
33X-RAY DIFFRACTION33chain 'F' and (resid 130 through 143 )F130 - 143
34X-RAY DIFFRACTION34chain 'F' and (resid 144 through 156 )F144 - 156
35X-RAY DIFFRACTION35chain 'F' and (resid 157 through 176 )F157 - 176
36X-RAY DIFFRACTION36chain 'F' and (resid 177 through 199 )F177 - 199
37X-RAY DIFFRACTION37chain 'F' and (resid 200 through 217 )F200 - 217
38X-RAY DIFFRACTION38chain 'G' and (resid 2 through 35 )G2 - 35
39X-RAY DIFFRACTION39chain 'G' and (resid 36 through 143 )G36 - 143
40X-RAY DIFFRACTION40chain 'G' and (resid 144 through 156 )G144 - 156
41X-RAY DIFFRACTION41chain 'G' and (resid 157 through 218 )G157 - 218
42X-RAY DIFFRACTION42chain 'H' and (resid 2 through 16 )H2 - 16
43X-RAY DIFFRACTION43chain 'H' and (resid 17 through 35 )H17 - 35
44X-RAY DIFFRACTION44chain 'H' and (resid 36 through 57 )H36 - 57
45X-RAY DIFFRACTION45chain 'H' and (resid 58 through 105 )H58 - 105
46X-RAY DIFFRACTION46chain 'H' and (resid 106 through 143 )H106 - 143
47X-RAY DIFFRACTION47chain 'H' and (resid 144 through 156 )H144 - 156
48X-RAY DIFFRACTION48chain 'H' and (resid 157 through 199 )H157 - 199
49X-RAY DIFFRACTION49chain 'H' and (resid 200 through 217 )H200 - 217
50X-RAY DIFFRACTION50chain 'I' and (resid 2 through 35 )I2 - 35
51X-RAY DIFFRACTION51chain 'I' and (resid 36 through 156 )I36 - 156
52X-RAY DIFFRACTION52chain 'I' and (resid 157 through 199 )I157 - 199
53X-RAY DIFFRACTION53chain 'I' and (resid 200 through 216 )I200 - 216
54X-RAY DIFFRACTION54chain 'J' and (resid 2 through 16 )J2 - 16
55X-RAY DIFFRACTION55chain 'J' and (resid 17 through 35 )J17 - 35
56X-RAY DIFFRACTION56chain 'J' and (resid 36 through 57 )J36 - 57
57X-RAY DIFFRACTION57chain 'J' and (resid 58 through 92 )J58 - 92
58X-RAY DIFFRACTION58chain 'J' and (resid 93 through 106 )J93 - 106
59X-RAY DIFFRACTION59chain 'J' and (resid 107 through 143 )J107 - 143
60X-RAY DIFFRACTION60chain 'J' and (resid 144 through 156 )J144 - 156
61X-RAY DIFFRACTION61chain 'J' and (resid 157 through 188 )J157 - 188
62X-RAY DIFFRACTION62chain 'J' and (resid 189 through 217 )J189 - 217
63X-RAY DIFFRACTION63chain 'K' and (resid 2 through 57 )K2 - 57
64X-RAY DIFFRACTION64chain 'K' and (resid 58 through 143 )K58 - 143
65X-RAY DIFFRACTION65chain 'K' and (resid 144 through 216 )K144 - 216
66X-RAY DIFFRACTION66chain 'L' and (resid 2 through 35 )L2 - 35
67X-RAY DIFFRACTION67chain 'L' and (resid 36 through 143 )L36 - 143
68X-RAY DIFFRACTION68chain 'L' and (resid 144 through 217 )L144 - 217
69X-RAY DIFFRACTION69chain 'M' and (resid 2 through 70 )M2 - 70
70X-RAY DIFFRACTION70chain 'M' and (resid 71 through 156 )M71 - 156
71X-RAY DIFFRACTION71chain 'M' and (resid 157 through 216 )M157 - 216
72X-RAY DIFFRACTION72chain 'N' and (resid 2 through 16 )N2 - 16
73X-RAY DIFFRACTION73chain 'N' and (resid 17 through 35 )N17 - 35
74X-RAY DIFFRACTION74chain 'N' and (resid 36 through 57 )N36 - 57
75X-RAY DIFFRACTION75chain 'N' and (resid 58 through 106 )N58 - 106
76X-RAY DIFFRACTION76chain 'N' and (resid 107 through 143 )N107 - 143
77X-RAY DIFFRACTION77chain 'N' and (resid 144 through 156 )N144 - 156
78X-RAY DIFFRACTION78chain 'N' and (resid 157 through 176 )N157 - 176
79X-RAY DIFFRACTION79chain 'N' and (resid 177 through 199 )N177 - 199
80X-RAY DIFFRACTION80chain 'N' and (resid 200 through 217 )N200 - 217
81X-RAY DIFFRACTION81chain 'O' and (resid 2 through 16 )O2 - 16
82X-RAY DIFFRACTION82chain 'O' and (resid 17 through 35 )O17 - 35
83X-RAY DIFFRACTION83chain 'O' and (resid 36 through 57 )O36 - 57
84X-RAY DIFFRACTION84chain 'O' and (resid 58 through 118 )O58 - 118
85X-RAY DIFFRACTION85chain 'O' and (resid 119 through 156 )O119 - 156
86X-RAY DIFFRACTION86chain 'O' and (resid 157 through 188 )O157 - 188
87X-RAY DIFFRACTION87chain 'O' and (resid 189 through 199 )O189 - 199
88X-RAY DIFFRACTION88chain 'O' and (resid 200 through 217 )O200 - 217
89X-RAY DIFFRACTION89chain 'P' and (resid 2 through 16 )P2 - 16
90X-RAY DIFFRACTION90chain 'P' and (resid 17 through 35 )P17 - 35
91X-RAY DIFFRACTION91chain 'P' and (resid 36 through 57 )P36 - 57
92X-RAY DIFFRACTION92chain 'P' and (resid 58 through 92 )P58 - 92
93X-RAY DIFFRACTION93chain 'P' and (resid 93 through 118 )P93 - 118
94X-RAY DIFFRACTION94chain 'P' and (resid 119 through 143 )P119 - 143
95X-RAY DIFFRACTION95chain 'P' and (resid 144 through 156 )P144 - 156
96X-RAY DIFFRACTION96chain 'P' and (resid 157 through 176 )P157 - 176
97X-RAY DIFFRACTION97chain 'P' and (resid 177 through 199 )P177 - 199
98X-RAY DIFFRACTION98chain 'P' and (resid 200 through 216 )P200 - 216
99X-RAY DIFFRACTION99chain 'Q' and (resid 2 through 70 )Q2 - 70
100X-RAY DIFFRACTION100chain 'Q' and (resid 71 through 136 )Q71 - 136
101X-RAY DIFFRACTION101chain 'Q' and (resid 137 through 217 )Q137 - 217
102X-RAY DIFFRACTION102chain 'R' and (resid 2 through 35 )R2 - 35
103X-RAY DIFFRACTION103chain 'R' and (resid 36 through 57 )R36 - 57
104X-RAY DIFFRACTION104chain 'R' and (resid 58 through 136 )R58 - 136
105X-RAY DIFFRACTION105chain 'R' and (resid 137 through 188 )R137 - 188
106X-RAY DIFFRACTION106chain 'R' and (resid 189 through 218 )R189 - 218
107X-RAY DIFFRACTION107chain 'S' and (resid 2 through 16 )S2 - 16
108X-RAY DIFFRACTION108chain 'S' and (resid 17 through 36 )S17 - 36
109X-RAY DIFFRACTION109chain 'S' and (resid 37 through 57 )S37 - 57
110X-RAY DIFFRACTION110chain 'S' and (resid 58 through 92 )S58 - 92
111X-RAY DIFFRACTION111chain 'S' and (resid 93 through 136 )S93 - 136
112X-RAY DIFFRACTION112chain 'S' and (resid 137 through 156 )S137 - 156
113X-RAY DIFFRACTION113chain 'S' and (resid 157 through 216 )S157 - 216
114X-RAY DIFFRACTION114chain 'T' and (resid 2 through 70 )T2 - 70
115X-RAY DIFFRACTION115chain 'T' and (resid 71 through 143 )T71 - 143
116X-RAY DIFFRACTION116chain 'T' and (resid 144 through 156 )T144 - 156
117X-RAY DIFFRACTION117chain 'T' and (resid 157 through 216 )T157 - 216
118X-RAY DIFFRACTION118chain 'U' and (resid 2 through 16 )U2 - 16
119X-RAY DIFFRACTION119chain 'U' and (resid 17 through 35 )U17 - 35
120X-RAY DIFFRACTION120chain 'U' and (resid 36 through 57 )U36 - 57
121X-RAY DIFFRACTION121chain 'U' and (resid 58 through 118 )U58 - 118
122X-RAY DIFFRACTION122chain 'U' and (resid 119 through 136 )U119 - 136
123X-RAY DIFFRACTION123chain 'U' and (resid 137 through 156 )U137 - 156
124X-RAY DIFFRACTION124chain 'U' and (resid 157 through 176 )U157 - 176
125X-RAY DIFFRACTION125chain 'U' and (resid 177 through 199 )U177 - 199
126X-RAY DIFFRACTION126chain 'U' and (resid 200 through 216 )U200 - 216
127X-RAY DIFFRACTION127chain 'V' and (resid 2 through 35 )V2 - 35
128X-RAY DIFFRACTION128chain 'V' and (resid 36 through 70 )V36 - 70
129X-RAY DIFFRACTION129chain 'V' and (resid 71 through 106 )V71 - 106
130X-RAY DIFFRACTION130chain 'V' and (resid 107 through 136 )V107 - 136
131X-RAY DIFFRACTION131chain 'V' and (resid 137 through 156 )V137 - 156
132X-RAY DIFFRACTION132chain 'V' and (resid 157 through 199 )V157 - 199
133X-RAY DIFFRACTION133chain 'V' and (resid 200 through 216 )V200 - 216
134X-RAY DIFFRACTION134chain 'W' and (resid 2 through 21 )W2 - 21
135X-RAY DIFFRACTION135chain 'W' and (resid 22 through 35 )W22 - 35
136X-RAY DIFFRACTION136chain 'W' and (resid 36 through 57 )W36 - 57
137X-RAY DIFFRACTION137chain 'W' and (resid 58 through 92 )W58 - 92
138X-RAY DIFFRACTION138chain 'W' and (resid 93 through 106 )W93 - 106
139X-RAY DIFFRACTION139chain 'W' and (resid 107 through 143 )W107 - 143
140X-RAY DIFFRACTION140chain 'W' and (resid 144 through 156 )W144 - 156
141X-RAY DIFFRACTION141chain 'W' and (resid 157 through 176 )W157 - 176
142X-RAY DIFFRACTION142chain 'W' and (resid 177 through 188 )W177 - 188
143X-RAY DIFFRACTION143chain 'W' and (resid 189 through 199 )W189 - 199
144X-RAY DIFFRACTION144chain 'W' and (resid 200 through 216 )W200 - 216
145X-RAY DIFFRACTION145chain 'X' and (resid 2 through 57 )X2 - 57
146X-RAY DIFFRACTION146chain 'X' and (resid 58 through 92 )X58 - 92
147X-RAY DIFFRACTION147chain 'X' and (resid 93 through 136 )X93 - 136
148X-RAY DIFFRACTION148chain 'X' and (resid 137 through 188 )X137 - 188
149X-RAY DIFFRACTION149chain 'X' and (resid 189 through 216 )X189 - 216

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  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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