[English] 日本語
Yorodumi
- PDB-5q09: Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5q09
TitleHuman liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosphate 1-phosphatase, E.C.3.1.3.11) complexed with the allosteric inhibitor 1-[4-bromo-6-(carbamoylamino)pyridin-2-yl]-3-[5-(2-methoxyethyl)-4-methylthiophen-2-yl]sulfonylurea
ComponentsFructose-1,6-bisphosphatase 1Fructose 1,6-bisphosphatase
KeywordsHYDROLASE/HYDROLASE inhibitor / D3R docking / HYDROLASE-HYDROLASE inhibitor complex
Function / homology
Function and homology information


cellular response to raffinose / sucrose biosynthetic process / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / negative regulation of Ras protein signal transduction / fructose 1,6-bisphosphate metabolic process / cellular response to magnesium ion / fructose 6-phosphate metabolic process ...cellular response to raffinose / sucrose biosynthetic process / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / negative regulation of Ras protein signal transduction / fructose 1,6-bisphosphate metabolic process / cellular response to magnesium ion / fructose 6-phosphate metabolic process / fructose metabolic process / Gluconeogenesis / monosaccharide binding / negative regulation of glycolytic process / cellular hyperosmotic salinity response / regulation of gluconeogenesis / AMP binding / dephosphorylation / cellular response to cAMP / response to nutrient levels / gluconeogenesis / negative regulation of cell growth / cellular response to insulin stimulus / cellular response to xenobiotic stimulus / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 ...Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-96A / Fructose-1,6-bisphosphatase 1 / Fructose-1,6-bisphosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
Model detailsFor D3R project
AuthorsRuf, A. / Joseph, C. / Alker, A. / Banner, D. / Tetaz, T. / Benz, J. / Kuhn, B. / Rudolph, M.G. / Yang, H. / Shao, C. / Burley, S.K.
CitationJournal: To be published
Title: Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosphate 1-phosphatase, E.C.3.1.3.11) complexed with the allosteric inhibitor 1-[4-bromo-6-(carbamoylamino)pyridin-2-yl]-3-[5-(2- ...Title: Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosphate 1-phosphatase, E.C.3.1.3.11) complexed with the allosteric inhibitor 1-[4-bromo-6-(carbamoylamino)pyridin-2-yl]-3-[5-(2-methoxyethyl)-4-methylthiophen-2-yl]sulfonylurea
Authors: Ruf, A. / Joseph, C. / Alker, A. / Banner, D. / Tetaz, T. / Benz, J. / Kuhn, B. / Rudolph, M.G.
History
DepositionApr 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Category: diffrn_radiation / Item: _diffrn_radiation.pdbx_diffrn_protocol
Revision 1.2Feb 6, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Feb 10, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fructose-1,6-bisphosphatase 1
B: Fructose-1,6-bisphosphatase 1
C: Fructose-1,6-bisphosphatase 1
D: Fructose-1,6-bisphosphatase 1
E: Fructose-1,6-bisphosphatase 1
F: Fructose-1,6-bisphosphatase 1
G: Fructose-1,6-bisphosphatase 1
H: Fructose-1,6-bisphosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,81416
Polymers294,8758
Non-polymers3,9398
Water31,2921737
1
A: Fructose-1,6-bisphosphatase 1
B: Fructose-1,6-bisphosphatase 1
C: Fructose-1,6-bisphosphatase 1
D: Fructose-1,6-bisphosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,4078
Polymers147,4384
Non-polymers1,9694
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16160 Å2
ΔGint-83 kcal/mol
Surface area44430 Å2
MethodPISA
2
E: Fructose-1,6-bisphosphatase 1
F: Fructose-1,6-bisphosphatase 1
G: Fructose-1,6-bisphosphatase 1
H: Fructose-1,6-bisphosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,4078
Polymers147,4384
Non-polymers1,9694
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16050 Å2
ΔGint-82 kcal/mol
Surface area44260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.579, 286.577, 83.616
Angle α, β, γ (deg.)90.000, 97.440, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 9 through 37 or resid 39...
21(chain B and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))
31(chain C and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))
41(chain D and (resid 9 through 37 or resid 39...
51(chain E and (resid 9 through 37 or resid 39...
61(chain F and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))
71(chain G and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))
81(chain H and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLEULEU(chain A and (resid 9 through 37 or resid 39...AA9 - 3710 - 38
12THRTHRGLYGLY(chain A and (resid 9 through 37 or resid 39...AA39 - 6140 - 62
13LYSLYSTYRTYR(chain A and (resid 9 through 37 or resid 39...AA72 - 13973 - 140
14LYSLYSSERSER(chain A and (resid 9 through 37 or resid 39...AA141 - 335142 - 336
21ASPASPLEULEU(chain B and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))BB9 - 3710 - 38
22THRTHRTYRTYR(chain B and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))BB39 - 13940 - 140
23LYSLYSSERSER(chain B and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))BB141 - 335142 - 336
31ASPASPLEULEU(chain C and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))CC9 - 3710 - 38
32THRTHRTYRTYR(chain C and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))CC39 - 13940 - 140
33LYSLYSSERSER(chain C and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))CC141 - 335142 - 336
41ASPASPLEULEU(chain D and (resid 9 through 37 or resid 39...DD9 - 3710 - 38
42THRTHRGLYGLY(chain D and (resid 9 through 37 or resid 39...DD39 - 6140 - 62
43LYSLYSTYRTYR(chain D and (resid 9 through 37 or resid 39...DD72 - 13973 - 140
44LYSLYSSERSER(chain D and (resid 9 through 37 or resid 39...DD141 - 335142 - 336
51ASPASPLEULEU(chain E and (resid 9 through 37 or resid 39...EE9 - 3710 - 38
52THRTHRGLYGLY(chain E and (resid 9 through 37 or resid 39...EE39 - 6140 - 62
53LYSLYSTYRTYR(chain E and (resid 9 through 37 or resid 39...EE72 - 13973 - 140
54LYSLYSSERSER(chain E and (resid 9 through 37 or resid 39...EE141 - 335142 - 336
61ASPASPLEULEU(chain F and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))FF9 - 3710 - 38
62THRTHRTYRTYR(chain F and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))FF39 - 13940 - 140
63LYSLYSSERSER(chain F and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))FF141 - 335142 - 336
71ASPASPLEULEU(chain G and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))GG9 - 3710 - 38
72THRTHRTYRTYR(chain G and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))GG39 - 13940 - 140
73LYSLYSSERSER(chain G and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))GG141 - 335142 - 336
81ASPASPLEULEU(chain H and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))HH9 - 3710 - 38
82THRTHRTYRTYR(chain H and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))HH39 - 13940 - 140
83LYSLYSSERSER(chain H and (resid 9 through 37 or resid 39 through 139 or resid 141 through 335))HH141 - 335142 - 336

-
Components

#1: Protein
Fructose-1,6-bisphosphatase 1 / Fructose 1,6-bisphosphatase / Growth-inhibiting protein 17 / cDNA FLJ75786 / highly similar to Homo sapiens fructose-1 / 6- ...Growth-inhibiting protein 17 / cDNA FLJ75786 / highly similar to Homo sapiens fructose-1 / 6-bisphosphatase 1 (FBP1) / mRNA


Mass: 36859.418 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBP1, hCG_1640493 / Production host: Escherichia coli (E. coli)
References: UniProt: Q2TU34, UniProt: P09467*PLUS, fructose-bisphosphatase
#2: Chemical
ChemComp-96A / N-{[4-bromo-6-(carbamoylamino)pyridin-2-yl]carbamoyl}-5-(2-methoxyethyl)-4-methylthiophene-2-sulfonamide


Mass: 492.368 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C15H18BrN5O5S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1737 / 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: 2.77 Å3/Da / Density % sol: 55.61 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M HEPES pH 7.0, 0.1M AMMONIUM ACETATE, 12%-25% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.987 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.9→29.388 Å / Num. obs: 237235 / % possible obs: 97.79 %

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.23data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→29.388 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.64 / Stereochemistry target values: ML
Details: THE INHIBITOR PYRIDINE GROUPS ARE NOT WELL ORDERED AND HAVE WEAK ELECTRON DENSITY AND HIGH B-FACTORS. THE ELECTRON DENSITY OF THE TERMINAL UREA LOOKS NOT COPLANAR WITH THE PYRIDINE.
RfactorNum. reflection% reflection
Rfree0.2061 11952 5.04 %
Rwork0.1678 225283 -
obs0.1697 237235 97.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.81 Å2 / Biso mean: 34.1321 Å2 / Biso min: 9.59 Å2
Refinement stepCycle: final / Resolution: 1.9→29.388 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19449 0 224 1737 21410
Biso mean--46.39 42.33 -
Num. residues----2541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00720065
X-RAY DIFFRACTIONf_angle_d0.89927111
X-RAY DIFFRACTIONf_chiral_restr0.0583056
X-RAY DIFFRACTIONf_plane_restr0.0063461
X-RAY DIFFRACTIONf_dihedral_angle_d11.61112181
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A12157X-RAY DIFFRACTION7.632TORSIONAL
12B12157X-RAY DIFFRACTION7.632TORSIONAL
13C12157X-RAY DIFFRACTION7.632TORSIONAL
14D12157X-RAY DIFFRACTION7.632TORSIONAL
15E12157X-RAY DIFFRACTION7.632TORSIONAL
16F12157X-RAY DIFFRACTION7.632TORSIONAL
17G12157X-RAY DIFFRACTION7.632TORSIONAL
18H12157X-RAY DIFFRACTION7.632TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.92160.32553150.28486365668083
1.9216-1.94420.31223790.27456672705187
1.9442-1.96790.30813740.26797046742092
1.9679-1.99280.29153850.24527596798198
1.9928-2.0190.27474060.230976758081100
2.019-2.04670.24854130.224576198032100
2.0467-2.07590.25484320.223877018133100
2.0759-2.10690.26283940.215776017995100
2.1069-2.13980.24374230.208377118134100
2.1398-2.17490.24163990.195776148013100
2.1749-2.21240.25623960.200377158111100
2.2124-2.25260.23913980.192975967994100
2.2526-2.29590.24774260.1976728098100
2.2959-2.34270.23464290.177675617990100
2.3427-2.39360.21413910.17147704809599
2.3936-2.44930.2224000.170476318031100
2.4493-2.51050.23264080.17467647805599
2.5105-2.57840.23164370.17657581801899
2.5784-2.65420.21894000.17057620802099
2.6542-2.73980.21053880.16057601798999
2.7398-2.83760.21463720.16567631800399
2.8376-2.95120.21064410.16067563800499
2.9512-3.08530.21753930.16137604799799
3.0853-3.24780.19833690.15267593796298
3.2478-3.4510.18713990.15277594799398
3.451-3.7170.16953890.13897525791498
3.717-4.09010.16994150.1387478789398
4.0901-4.67990.14744150.12977489790497
4.6799-5.88840.15663570.13757539789697
5.8884-29.39130.1924090.16327339774895
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)
10.33910.13210.07480.2986-0.26340.1873-0.0452-0.02110.0755-0.1754-0.0247-0.0827-0.03890.0278-0.01170.24940.02540.01970.14870.01870.185338.111316.0757-5.4571
20.5368-0.0475-0.12370.4179-0.01390.1349-0.01540.04610.0725-0.19520.01640.0733-0.06430.02240.0240.27810.0414-0.05630.13170.02430.152220.447622.9597-7.7857
30.2365-0.0512-0.08390.0698-0.02440.22740.001-0.01110.0916-0.13410.05080.1038-0.1539-0.05950.06190.36490.0438-0.08120.13830.03250.229118.769931.4471-10.1481
40.2352-0.2414-0.12660.6167-0.14310.1811-0.0918-0.1021-0.1515-0.02260.0180.24790.11030.0572-0.0350.06950.02020.02660.1960.03360.264313.0713-2.998715.9653
50.4615-0.3593-0.02040.5726-0.07940.212-0.0053-0.1148-0.06580.02150.03030.192-0.126-0.00470.00280.11910.05590.02120.1658-0.00770.19799.657315.569616.3465
60.1576-0.1452-0.06130.20330.01680.5672-0.0332-0.1522-0.2253-0.04480.1060.3231-0.6140.02410.0590.01990.17160.02490.20190.00880.3581.547819.140117.8089
70.3426-0.0943-0.26730.20870.19750.49080.02470.0619-0.051-0.1244-0.04190.0413-0.0615-0.07990.01140.20180.03980.01680.13960.01760.097536.5007-9.1632-11.5066
80.2978-0.16810.00270.391-0.18160.60570.03480.0590.037-0.1415-0.0425-0.09580.02580.1229-0.00530.13670.0250.04430.15560.01040.116754.2941-18.9748-7.1492
90.0473-0.08760.09550.2143-0.17840.1658-0.05850.1049-0.00280.1834-0.00340.2921-0.1595-0.32930.00060.1374-0.00320.0710.33680.06410.255320.1541-13.375426.615
10-0.0719-0.0608-0.12260.10530.02310.09360.0204-0.05120.05490.11030.0308-0.012-0.14640.045200.15260.02270.02870.16120.01530.136340.7409-1.943423.0061
110.0346-0.03470.06480.4496-0.13150.13180.0121-0.04670.08550.16180.0026-0.0685-0.05890.165-0.00550.21870.03090.01750.20210.01930.110842.3071-10.224931.0737
120.2203-0.21030.07620.4538-0.18070.5016-0.0252-0.0447-0.07840.055-0.00140.0730.12990.0118-0.03340.13020.01710.0080.13270.02950.1442.0208-25.834415.8326
130.1798-0.1056-0.1480.20080.09610.1592-0.0179-0.04910.0120.02630.0512-0.05660.05720.050600.16830.04320.00040.15520.02420.129948.002-27.228124.7543
140.28810.01210.10320.2645-0.14340.21330.0298-0.0328-0.11530.1472-0.023-0.04490.01930.1252-0.00050.23420.0126-0.03640.16650.02160.2127-0.258651.650742.929
150.2773-0.16-0.1660.11140.00410.08790.0907-0.0044-0.3847-0.03960.03810.10290.26330.0749-0.01090.3190.0109-0.03830.17750.08890.3199-2.356741.207346.4208
160.3529-0.1491-0.05610.21280.02120.33830.006-0.1863-0.22880.2142-0.00290.117-0.0213-0.08930.00870.1263-0.03230.03580.17340.05740.3183-22.889645.528940.1925
170.18980.01560.10190.01760.05390.15430.2222-0.0907-0.3860.1804-0.1144-0.06730.2526-0.17310.03820.3165-0.0727-0.03120.17150.07170.4796-20.384935.725243.4968
180.47280.18820.06320.3671-0.0170.25750.01170.15230.07050.0010.00210.1341-0.0435-0.02480.00690.11020.0162-0.02130.1567-0.00580.1522-18.447169.882916.5376
190.73740.1773-0.41450.19590.24830.14320.02590.3206-0.2213-0.0391-0.1430.08330.00630.1038-0.09870.1157-0.0027-0.03710.121-0.13520.2584-22.169851.291215.5114
200.11110.1414-0.03730.2113-0.10270.0670.00010.2739-0.29370.0410.00360.22360.0458-0.02960.04120.1582-0.0041-0.04570.2659-0.14220.3979-29.778648.072412.1434
210.0181-0.0086-0.01510.0202-0.02540.014-0.231-0.0448-0.250.312-0.1817-0.23260.2066-0.01410.00010.41420.02390.00810.24720.04050.24717.045360.133255.2705
220.07610.03890.02540.00950.03220.07480.0057-0.01830.05950.1519-0.01480.1641-0.0917-0.02020.0020.155-0.0115-0.00490.1146-0.00640.1174-6.242676.030343.4724
230.0241-0.0058-0.01480.04260.04730.03150.0874-0.07290.06050.0396-0.06130.1760.0538-0.1483-00.2455-0.02840.01770.2037-0.00270.1459-6.382783.463157.815
240.1293-0.14240.01450.12030.04460.05340.0716-0.00650.1717-0.11120.05180.0532-0.1358-0.11590.00190.274-0.03710.00690.19750.02470.1171-1.137282.01649.3439
250.11410.04290.01320.03840.01180.00710.1347-0.06040.11810.1462-0.0280.0866-0.09350.07970.0040.2539-0.0320.00740.1867-0.01940.10321.393280.074162.1868
260.2627-0.02880.0960.4874-0.27820.12890.0082-0.0347-0.03790.1141-0.0548-0.01060.11920.0894-0.01090.1336-0.0096-0.03580.15440.0120.077711.877975.338648.249
270.0189-0.04670.0180.0956-0.12780.1194-0.0717-0.09110.00430.1123-0.057-0.023-0.09450.12900.1609-0.0669-0.02720.25470.01440.190426.049295.3540.8501
28-0.0115-0.0121-0.0634-0.00870.03250.11460.1544-0.04560.05890.0948-0.0827-0.0122-0.29230.08620.00010.2726-0.03120.00060.1913-0.00010.158313.85787.543848.4895
290.09650.1121-0.05770.2857-0.12820.08440.0517-0.01530.02240.3118-0.0883-0.0493-0.28290.1621-0.0250.2149-0.1041-0.07370.2634-0.00660.138420.201391.066655.3458
300.0085-0.02880.00720.08310.00080.0733-0.12120.1397-0.0272-0.1401-0.02760.24070.0049-0.2344-0.00820.19130.0098-0.06420.29970.00470.1715-8.797880.16658.1798
31-0.0095-0.01050.084-0.0161-0.08130.0365-0.07270.068-0.08-0.00470.0054-0.05990.1370.0523-00.17950.0118-0.00590.1609-0.00360.13417.227567.681520.3924
320.11080.147-0.10080.0908-0.07780.05460.06770.0241-0.0736-0.0399-0.0938-0.12210.21570.1203-00.2730.01030.01620.2258-0.01480.130414.104671.97397.8492
33-0.07350.1026-0.01070.1671-0.02740.0150.0811-0.0192-0.0567-0.11260.0364-0.07020.07750.22160.02020.21670.02750.02280.18390.00580.088214.841478.43710.8143
340.1801-0.13360.02260.40140.0385-0.00830.05980.05950.0491-0.08060.00960.088-0.0786-0.01060.00630.14260.0093-0.01150.15150.02720.10812.465386.544120.2383
350.03710.02-0.01530.027-0.01130.00070.1083-0.1098-0.0224-0.1359-0.1271-0.0932-0.2970.3168-0.00060.1987-0.06010.02720.26730.03910.249725.3628100.831628.7987
360.06520.05960.06230.0804-0.0050.16090.05890.0425-0.01640.01390.0687-0.113-0.06050.04930.00040.1891-0.030.02620.1444-0.02760.138616.54595.383927.1072
370.05240.01410.12220.13-0.06590.25910.02150.0467-0.0473-0.0670.0012-0.0886-0.01640.094800.2066-0.01690.04040.1820.01330.159617.737994.502414.6649
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 122 )A9 - 122
2X-RAY DIFFRACTION2chain 'A' and (resid 123 through 247 )A123 - 247
3X-RAY DIFFRACTION3chain 'A' and (resid 248 through 335 )A248 - 335
4X-RAY DIFFRACTION4chain 'B' and (resid 9 through 122 )B9 - 122
5X-RAY DIFFRACTION5chain 'B' and (resid 123 through 247 )B123 - 247
6X-RAY DIFFRACTION6chain 'B' and (resid 248 through 335 )B248 - 335
7X-RAY DIFFRACTION7chain 'C' and (resid 9 through 131 )C9 - 131
8X-RAY DIFFRACTION8chain 'C' and (resid 132 through 335 )C132 - 335
9X-RAY DIFFRACTION9chain 'D' and (resid 9 through 28 )D9 - 28
10X-RAY DIFFRACTION10chain 'D' and (resid 29 through 106 )D29 - 106
11X-RAY DIFFRACTION11chain 'D' and (resid 107 through 155 )D107 - 155
12X-RAY DIFFRACTION12chain 'D' and (resid 156 through 247 )D156 - 247
13X-RAY DIFFRACTION13chain 'D' and (resid 248 through 335 )D248 - 335
14X-RAY DIFFRACTION14chain 'E' and (resid 9 through 106 )E9 - 106
15X-RAY DIFFRACTION15chain 'E' and (resid 107 through 155 )E107 - 155
16X-RAY DIFFRACTION16chain 'E' and (resid 156 through 247 )E156 - 247
17X-RAY DIFFRACTION17chain 'E' and (resid 248 through 335 )E248 - 335
18X-RAY DIFFRACTION18chain 'F' and (resid 9 through 122 )F9 - 122
19X-RAY DIFFRACTION19chain 'F' and (resid 123 through 247 )F123 - 247
20X-RAY DIFFRACTION20chain 'F' and (resid 248 through 335 )F248 - 335
21X-RAY DIFFRACTION21chain 'G' and (resid 9 through 28 )G9 - 28
22X-RAY DIFFRACTION22chain 'G' and (resid 29 through 88 )G29 - 88
23X-RAY DIFFRACTION23chain 'G' and (resid 89 through 106 )G89 - 106
24X-RAY DIFFRACTION24chain 'G' and (resid 107 through 131 )G107 - 131
25X-RAY DIFFRACTION25chain 'G' and (resid 132 through 148 )G132 - 148
26X-RAY DIFFRACTION26chain 'G' and (resid 149 through 212 )G149 - 212
27X-RAY DIFFRACTION27chain 'G' and (resid 213 through 247 )G213 - 247
28X-RAY DIFFRACTION28chain 'G' and (resid 248 through 290 )G248 - 290
29X-RAY DIFFRACTION29chain 'G' and (resid 291 through 335 )G291 - 335
30X-RAY DIFFRACTION30chain 'H' and (resid 9 through 28 )H9 - 28
31X-RAY DIFFRACTION31chain 'H' and (resid 29 through 88 )H29 - 88
32X-RAY DIFFRACTION32chain 'H' and (resid 89 through 122 )H89 - 122
33X-RAY DIFFRACTION33chain 'H' and (resid 123 through 155 )H123 - 155
34X-RAY DIFFRACTION34chain 'H' and (resid 156 through 212 )H156 - 212
35X-RAY DIFFRACTION35chain 'H' and (resid 213 through 231 )H213 - 231
36X-RAY DIFFRACTION36chain 'H' and (resid 232 through 274 )H232 - 274
37X-RAY DIFFRACTION37chain 'H' and (resid 275 through 335 )H275 - 335

+
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