[English] 日本語
Yorodumi
- PDB-5k0b: Crystal Structure of COMT in complex with 2,4-dimethyl-5-[3-(1-ph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5k0b
TitleCrystal Structure of COMT in complex with 2,4-dimethyl-5-[3-(1-phenylethyl)-1H-pyrazol-5-yl]-1,3-thiazole
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 / catecholamine catabolic process / catechol O-methyltransferase activity / S-adenosylhomocysteine metabolic process ...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 / catecholamine catabolic process / catechol O-methyltransferase activity / S-adenosylhomocysteine metabolic process / catechol O-methyltransferase / developmental process / renal sodium excretion / renal filtration / dopamine secretion / renin secretion into blood stream / negative regulation of dopamine metabolic process / fear response / catecholamine metabolic process / renal albumin absorption / artery development / habituation / short-term memory / cerebellar cortex morphogenesis / S-adenosylmethionine metabolic process / response to salt / dopamine catabolic process / cellular response to phosphate starvation / glomerulus development / norepinephrine metabolic process / synaptic transmission, dopaminergic / response to angiotensin / cellular response to cocaine / estrogen metabolic process / cholesterol efflux / response to stress / response to food / exploration behavior / response to temperature stimulus / response to corticosterone / prostaglandin metabolic process / glycogen metabolic process / response to pain / startle response / dopamine metabolic process / detection of temperature stimulus involved in sensory perception of pain / behavioral fear response / multicellular organismal response to stress / response to amphetamine / response to cytokine / kidney development / learning / female pregnancy / negative regulation of smooth muscle cell proliferation / visual learning / multicellular organism growth / response to organic cyclic compound / memory / response to toxic substance / cognition / regulation of blood pressure / response to wounding / response to estrogen / gene expression / cell body / postsynaptic membrane / vesicle / postsynapse / methylation / 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 / Class I-like SAM-dependent O-methyltransferase / 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-6PS / : / PHOSPHATE ION / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.36 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.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.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.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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,65856
Polymers194,5508
Non-polymers6,10748
Water12,412689
1
A: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9657
Polymers24,3191
Non-polymers6476
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0969
Polymers24,3191
Non-polymers7778
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3719
Polymers24,3191
Non-polymers1,0538
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0827
Polymers24,3191
Non-polymers7636
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2508
Polymers24,3191
Non-polymers9317
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9184
Polymers24,3191
Non-polymers6003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8875
Polymers24,3191
Non-polymers5684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0887
Polymers24,3191
Non-polymers7696
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)222.095, 222.095, 123.085
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Catechol O-methyltransferase


Mass: 24318.801 Da / Num. of mol.: 8
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

-
Non-polymers , 7 types, 737 molecules

#2: Chemical
ChemComp-6PS / 2,4-dimethyl-5-{3-[(1R)-1-phenylethyl]-1H-pyrazol-5-yl}-1,3-thiazole


Mass: 283.391 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C16H17N3S
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 689 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.52 Å3/Da / Density % sol: 72.76 %
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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 2.36→48.95 Å / Num. obs: 141537 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Biso Wilson estimate: 51.72 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.187 / Net I/σ(I): 11.09
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.36-2.422.0091.19199.9
2.42-2.491.7131.43199.9
2.49-2.561.4581.73199.9
2.56-2.641.1942.19199.9
2.64-2.730.9942.74199.9
2.73-2.820.8153.51199.9
2.82-2.930.6684.311100
2.93-3.050.5275.51199.9
3.05-3.180.387.371100
3.18-3.340.26810.161100
3.34-3.520.19313.591100
3.52-3.730.1417.49199.9
3.73-3.990.11320.31100
3.99-4.310.08524.621100
4.31-4.720.07129.31100
4.72-5.280.07428.241100
5.28-6.090.08225.031100
6.09-7.460.0729.11100
7.46-10.550.04540.25199.6
10.550.03846.07198.6

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
PHENIXrefinement
XDSdata reduction
PHENIXphasing
RefinementResolution: 2.36→48.085 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.62
RfactorNum. reflection% reflection
Rfree0.195 7089 5.01 %
Rwork0.1547 --
obs0.1567 141376 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 158.96 Å2 / Biso mean: 51.5309 Å2 / Biso min: 17.79 Å2
Refinement stepCycle: final / Resolution: 2.36→48.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13494 0 368 689 14551
Biso mean--56.77 48.71 -
Num. residues----1722
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)
15.5138-0.737-1.14084.34661.75575.28020.04580.27660.1336-0.41510.01630.5549-0.2133-0.1673-0.07630.485-0.06850.00010.27160.04280.371985.003350.2489-18.9878
28.22511.7966-2.03372.3182-0.68891.4748-0.60610.02660.3072-0.62040.23620.3735-0.07270.13120.41860.56-0.0419-0.01570.28550.00830.246794.435462.2206-18.2622
31.94430.41740.42581.75120.62662.0427-0.18590.0776-0.2659-0.18920.0954-0.04770.33590.21260.08780.47010.01630.09060.2908-0.00060.28101.337153.9128-13.8681
41.9851.40590.89343.11121.11142.05410.0159-0.0747-0.40970.21840.0461-0.24920.38730.1327-0.06040.41030.03170.06090.27780.06460.3189102.34150.7313-7.7953
58.0712-2.23620.02324.35020.86323.2835-0.0622-0.5864-0.11650.81130.0206-0.10830.00520.21190.01950.5180.0213-0.01480.30220.06990.2096104.264263.94010.8149
61.7906-0.09810.91911.6936-0.1921.8625-0.1102-0.0747-0.04650.0486-0.026-0.1994-0.11170.04420.12590.3097-0.00930.05260.23520.01890.1931104.310970.1428-7.4393
73.6191-1.1047-3.01563.34820.21423.4344-0.4126-0.3114-0.39650.2230.0790.38930.34390.39370.28810.2483-0.04360.0080.35860.04410.306275.796772.8795-1.7739
86.37521.89471.34020.65290.57742.1372-0.42390.32461.0406-0.16920.15140.2289-0.5415-0.14190.24810.30180.069-0.03020.2506-0.02610.406566.346541.81011.9216
97.92572.1364-4.34235.7619-1.76167.5509-0.19680.7792-0.5191-0.65860.00550.58440.2798-0.51640.20570.35720.0617-0.1360.3284-0.11680.455159.479733.7405-2.7529
102.10462.4914-0.77186.972-1.60321.75570.15310.0588-0.1211-0.6106-0.32650.4610.027-0.09050.15430.34380.0487-0.05030.3038-0.09010.428364.73722.3797-2.4815
111.1398-0.46610.96251.533-0.03461.39620.0448-0.07890.18940.0538-0.14320.44270.1314-0.20310.10210.30830.01340.03620.303-0.08520.454263.61922.90388.9144
120.732-0.16890.5940.0743-0.19870.5442-0.1420.2334-0.051-0.19950.0370.2108-0.07950.00990.05590.27640.0560.02050.3046-0.10570.39764.250534.97289.9082
139.3452-3.34462.3832.9527-1.30663.2419-0.2826-0.8483-0.0920.46390.1210.5632-0.0403-0.51670.14090.32780.00360.0770.3373-0.12130.471562.915627.414614.8504
143.23710.9328-0.15523.18880.02352.47090.0946-0.322-0.00710.4623-0.02530.11250.15080.0013-0.05320.30330.01440.03290.2146-0.04710.270374.241916.724314.4299
151.0258-0.4986-0.11540.45710.43142.4150.0665-0.0692-0.12750.1475-0.02080.1717-0.02560.06630.00720.2795-0.02720.03980.1898-0.04250.350872.571512.76825.5668
163.5939-2.50922.31212.0327-1.34874.09270.2275-0.116-0.2973-0.05610.08320.25410.21660.0898-0.3320.37810.00290.03460.2369-0.06650.360976.05327.1450.8836
171.33752.0953-0.80213.2269-0.87431.83940.0523-0.1291-0.0269-0.44660.0081-0.25770.09560.1911-0.04620.52360.00360.0770.29210.00590.673287.681628.7093-14.814
186.7052-2.21480.05483.09071.15922.56690.04351.12860.1139-0.42250.13330.4770.0928-0.3828-0.14750.3918-0.0742-0.05740.57920.09710.345166.529779.4793-22.9063
193.54051.19510.02292.27-0.05581.20730.08220.20580.34010.09280.02730.4387-0.0124-0.1817-0.1080.32070.00320.0630.35950.07270.378566.295882.5252-7.6207
206.72961.72292.89680.44450.72031.2708-0.33061.00970.973-0.44660.23130.168-0.17980.02350.08410.3732-0.03680.00850.4430.2130.447970.092289.1299-18.6617
219.6871.10014.92834.56690.67195.9478-0.21960.1260.9763-0.13060.35720.3547-0.9277-0.1979-0.05430.43510.02450.12470.37750.14330.510168.379993.3808-10.9718
224.4858-0.1751-2.00082.96080.17473.42170.4583-0.16470.68770.3293-0.07950.1208-0.60750.0618-0.3940.4329-0.0140.16280.32890.01060.412975.008591.885-0.1978
233.5380.19450.95226.25570.51570.29480.2867-0.44190.3491-0.03740.0805-0.0853-0.40420.4112-0.38840.326-0.02990.07840.44190.02220.286281.036684.06263.8757
241.7316-0.1457-0.42352.5993-0.01920.83240.1468-0.50160.1198-0.10.06910.0231-0.23280.2832-0.21310.34-0.00450.07920.40620.01840.297273.192580.53563.3864
254.8480.59741.09034.04990.90063.9783-0.3192-0.6383-0.46220.52370.11630.3361-0.15940.37640.2120.4444-0.01480.12910.44730.11090.323874.592774.25288.5465
261.5988-1.113-0.69221.6239-0.29231.29120.1776-0.2581-0.04730.1519-0.0993-0.06770.00780.0483-0.09270.3367-0.060.02380.25920.06140.252295.358370.5673-10.3453
273.79020.35571.52532.2766-0.83057.1615-0.25810.27330.32310.4732-0.0842-0.5295-0.42611.33610.35160.4852-0.0979-0.17320.55750.07730.5046121.479882.032812.2783
282.5980.39361.43962.69260.83043.6786-0.075-0.44390.27230.7359-0.3135-0.1623-0.0735-0.1440.36550.6163-0.0875-0.10260.4801-0.01130.3504108.708582.813618.0848
292.5039-0.2078-1.00731.2757-0.01652.1013-0.2627-0.56240.06260.4911-0.49860.8970.6276-1.0450.58470.6677-0.1560.11630.8828-0.25760.481793.638680.837415.1639
302.1036-0.6873-0.23662.20290.17883.4938-0.2357-0.3730.63240.2061-0.60460.7929-0.8322-1.5010.65890.66830.155-0.14120.8133-0.37930.691494.049893.97213.6091
311.5417-0.4509-0.52621.9024-1.07411.9306-0.2276-0.0291-0.02170.19680.1385-0.2508-0.32920.12540.19440.33110.0268-0.01750.22690.02130.2658100.463385.7308-12.421
322.7257-0.6389-1.30522.5799-1.78756.4137-0.53380.86230.15-1.76140.6931.2162-0.0144-0.5791-0.24611.2412-0.3443-0.4070.82480.21060.828572.732129.0874-34.5074
333.91020.9591.88823.9305-0.54992.3376-0.5910.1337-0.0397-1.00380.56910.10630.2315-0.52730.00670.8095-0.10530.00860.45810.04280.425284.701633.7259-26.5664
340.25990.5424-0.30632.048-1.33391.0305-0.56780.7735-0.9303-2.84970.7101-0.98230.9029-0.25130.33611.6551-0.24330.53080.5612-0.29840.630789.417320.3238-31.9772
350.4543-0.9094-0.14092.2706-0.31361.8159-0.17710.1886-0.5799-0.4396-0.3081-1.54490.29110.37650.42090.5359-0.00440.24870.34550.05020.944996.233424.499-16.4055
363.48460.7617-0.74020.35020.27851.17990.22650.07050.0568-0.1827-0.0510.72460.19680.449-0.2510.3799-0.0086-0.01890.2132-0.07630.294274.074314.8626-3.4229
374.3691-0.5116-0.95434.04330.435.88250.0654-0.58890.27870.83480.0331-1.16760.0070.7254-0.07520.4252-0.0545-0.23320.4570.04030.5563118.1981102.3772-15.5674
382.77021.37781.05055.17712.06365.76750.0204-0.3325-0.13330.4469-0.3708-0.59840.00410.03920.33140.3107-0.0128-0.04370.35870.08420.3989110.193489.4492-17.4973
392.90740.0880.14113.5435-0.3260.8128-0.09540.15940.1453-0.09750.0332-0.1804-0.00380.07920.0450.2532-0.0235-0.02350.29870.04560.2071103.061598.9324-26.7094
404.24871.01820.51395.9171.22339.6007-0.11020.24090.30510.04040.19570.5915-0.1917-0.17550.00350.23850.00880.03930.28630.09070.282789.173493.1711-20.1076
412.0688-0.1646-0.57381.6325-1.25291.5738-0.0750.0037-0.0710.01150.1030.07950.1659-0.0627-0.02870.3264-0.0140.00780.28050.01920.21994.345584.3538-19.3236
421.68680.07760.29033.9541.8163.6823-0.0895-0.45310.67290.0235-0.2260.2603-1.2165-0.53360.14750.66040.1487-0.17370.4909-0.12840.5678100.993993.63487.6855
437.0581.4528-0.74723.0721-1.02173.06520.0701-0.5482-0.13650.04660.0585-0.26540.18840.3947-0.08130.3801-0.0264-0.0850.2802-0.0780.554972.768-22.6594-9.9858
444.283-2.40.58642.58770.42841.2383-0.00080.241-0.3970.1773-0.11760.1181-0.13780.02860.11420.4312-0.055-0.03150.2859-0.07780.571769.6268-7.8632-8.8033
452.03380.57030.20443.3150.36161.381-0.12370.3639-0.1242-1.05960.1390.4027-0.1711-0.0452-0.02680.6695-0.0655-0.1450.3365-0.0980.500465.7857-10.3779-23.0274
462.39351.23670.38221.98-0.37962.1447-0.16550.28360.1123-0.92730.13090.346-0.340.01610.00890.6914-0.0614-0.08540.2756-0.07050.444971.58965.7092-19.8359
475.8594-0.4446-0.04531.80191.64211.54220.13460.3995-0.654-0.08120.0448-0.3428-0.03950.1131-0.19970.3670.04110.00710.2834-0.08150.453696.206-3.5912-7.8476
485.24630.00511.40483.0659-0.8544.68120.2452-0.9225-0.77610.41970.14880.22220.59370.0573-0.38440.51070.0473-0.02120.72220.19690.56591.2059-9.524413.3655
494.01810.2917-0.01742.4015-1.04772.14390.148-1.01530.03840.40190.0661-0.3679-0.07450.5267-0.22760.38640.0047-0.07810.5598-0.12410.3911102.03810.36138.3632
503.4185-1.011-0.75952.0717-0.73462.31760.2739-0.3510.72460.113-0.0447-0.3566-0.47540.4524-0.1880.3862-0.05190.05220.3495-0.15910.5627101.67448.5843-3.298
511.98710.68660.55244.9186-1.2432.81150.08550.2284-0.0085-0.25150.0011-0.2409-0.19730.2531-0.0910.34860.01480.10130.3489-0.10310.4237103.63810.1389-14.2482
522.50371.80680.17761.95790.48060.87480.03930.11980.1669-0.69070.00170.14670.1050.0393-0.08950.54830.0012-0.00550.2807-0.09760.338575.73551.6011-11.2978
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 35 )A3 - 35
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 57 )A36 - 57
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 92 )A58 - 92
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 143 )A93 - 143
5X-RAY DIFFRACTION5chain 'A' and (resid 144 through 156 )A144 - 156
6X-RAY DIFFRACTION6chain 'A' and (resid 157 through 195 )A157 - 195
7X-RAY DIFFRACTION7chain 'A' and (resid 196 through 216 )A196 - 216
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 16 )B2 - 16
9X-RAY DIFFRACTION9chain 'B' and (resid 17 through 35 )B17 - 35
10X-RAY DIFFRACTION10chain 'B' and (resid 36 through 57 )B36 - 57
11X-RAY DIFFRACTION11chain 'B' and (resid 58 through 92 )B58 - 92
12X-RAY DIFFRACTION12chain 'B' and (resid 93 through 106 )B93 - 106
13X-RAY DIFFRACTION13chain 'B' and (resid 107 through 118 )B107 - 118
14X-RAY DIFFRACTION14chain 'B' and (resid 119 through 156 )B119 - 156
15X-RAY DIFFRACTION15chain 'B' and (resid 157 through 176 )B157 - 176
16X-RAY DIFFRACTION16chain 'B' and (resid 177 through 195 )B177 - 195
17X-RAY DIFFRACTION17chain 'B' and (resid 196 through 216 )B196 - 216
18X-RAY DIFFRACTION18chain 'C' and (resid 3 through 35 )C3 - 35
19X-RAY DIFFRACTION19chain 'C' and (resid 36 through 92 )C36 - 92
20X-RAY DIFFRACTION20chain 'C' and (resid 93 through 106 )C93 - 106
21X-RAY DIFFRACTION21chain 'C' and (resid 107 through 118 )C107 - 118
22X-RAY DIFFRACTION22chain 'C' and (resid 119 through 143 )C119 - 143
23X-RAY DIFFRACTION23chain 'C' and (resid 144 through 156 )C144 - 156
24X-RAY DIFFRACTION24chain 'C' and (resid 157 through 176 )C157 - 176
25X-RAY DIFFRACTION25chain 'C' and (resid 177 through 195 )C177 - 195
26X-RAY DIFFRACTION26chain 'C' and (resid 196 through 218 )C196 - 218
27X-RAY DIFFRACTION27chain 'D' and (resid 3 through 35 )D3 - 35
28X-RAY DIFFRACTION28chain 'D' and (resid 36 through 118 )D36 - 118
29X-RAY DIFFRACTION29chain 'D' and (resid 119 through 156 )D119 - 156
30X-RAY DIFFRACTION30chain 'D' and (resid 157 through 195 )D157 - 195
31X-RAY DIFFRACTION31chain 'D' and (resid 196 through 218 )D196 - 218
32X-RAY DIFFRACTION32chain 'E' and (resid 3 through 35 )E3 - 35
33X-RAY DIFFRACTION33chain 'E' and (resid 36 through 57 )E36 - 57
34X-RAY DIFFRACTION34chain 'E' and (resid 58 through 143 )E58 - 143
35X-RAY DIFFRACTION35chain 'E' and (resid 144 through 195 )E144 - 195
36X-RAY DIFFRACTION36chain 'E' and (resid 196 through 219 )E196 - 219
37X-RAY DIFFRACTION37chain 'F' and (resid 3 through 35 )F3 - 35
38X-RAY DIFFRACTION38chain 'F' and (resid 36 through 57 )F36 - 57
39X-RAY DIFFRACTION39chain 'F' and (resid 58 through 143 )F58 - 143
40X-RAY DIFFRACTION40chain 'F' and (resid 144 through 156 )F144 - 156
41X-RAY DIFFRACTION41chain 'F' and (resid 157 through 195 )F157 - 195
42X-RAY DIFFRACTION42chain 'F' and (resid 196 through 216 )F196 - 216
43X-RAY DIFFRACTION43chain 'G' and (resid 3 through 35 )G3 - 35
44X-RAY DIFFRACTION44chain 'G' and (resid 36 through 57 )G36 - 57
45X-RAY DIFFRACTION45chain 'G' and (resid 58 through 143 )G58 - 143
46X-RAY DIFFRACTION46chain 'G' and (resid 144 through 195 )G144 - 195
47X-RAY DIFFRACTION47chain 'G' and (resid 196 through 216 )G196 - 216
48X-RAY DIFFRACTION48chain 'H' and (resid 3 through 42 )H3 - 42
49X-RAY DIFFRACTION49chain 'H' and (resid 43 through 118 )H43 - 118
50X-RAY DIFFRACTION50chain 'H' and (resid 119 through 176 )H119 - 176
51X-RAY DIFFRACTION51chain 'H' and (resid 177 through 195 )H177 - 195
52X-RAY DIFFRACTION52chain 'H' and (resid 196 through 218 )H196 - 218

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • 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

-
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

Read more