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- PDB-5q0j: Ligand binding to FARNESOID-X-RECEPTOR -

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Basic information

Entry
Database: PDB / ID: 5q0j
TitleLigand binding to FARNESOID-X-RECEPTOR
Components
  • Bile acid receptor
  • COACTIVATOR PEPTIDE SRC-1 HD3
KeywordsTRANSCRIPTION / D3R / FXR / Docking
Function / homology
Function and homology information


regulation of urea metabolic process / intracellular bile acid receptor signaling pathway / chenodeoxycholic acid binding / positive regulation of phosphatidic acid biosynthetic process / positive regulation of glutamate metabolic process / positive regulation of ammonia assimilation cycle / bile acid receptor activity / regulation of low-density lipoprotein particle clearance / intracellular triglyceride homeostasis / cellular response to bile acid ...regulation of urea metabolic process / intracellular bile acid receptor signaling pathway / chenodeoxycholic acid binding / positive regulation of phosphatidic acid biosynthetic process / positive regulation of glutamate metabolic process / positive regulation of ammonia assimilation cycle / bile acid receptor activity / regulation of low-density lipoprotein particle clearance / intracellular triglyceride homeostasis / cellular response to bile acid / negative regulation of very-low-density lipoprotein particle remodeling / negative regulation of interleukin-1 production / regulation of bile acid biosynthetic process / regulation of insulin secretion involved in cellular response to glucose stimulus / cellular response to organonitrogen compound / toll-like receptor 9 signaling pathway / negative regulation of monocyte chemotactic protein-1 production / intracellular receptor signaling pathway / bile acid metabolic process / nitrogen catabolite activation of transcription from RNA polymerase II promoter / labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / bile acid binding / cell-cell junction assembly / positive regulation of female receptivity / bile acid signaling pathway / negative regulation of interleukin-2 production / cellular response to fatty acid / regulation of cholesterol metabolic process / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / positive regulation of interleukin-17 production / intracellular glucose homeostasis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of interleukin-6 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / cellular response to Thyroglobulin triiodothyronine / estrous cycle / Synthesis of bile acids and bile salts / negative regulation of tumor necrosis factor-mediated signaling pathway / fatty acid homeostasis / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / negative regulation of canonical NF-kappaB signal transduction / positive regulation of insulin receptor signaling pathway / response to retinoic acid / histone acetyltransferase activity / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / Notch signaling pathway / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / lactation / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / response to progesterone / cholesterol homeostasis / transcription coregulator binding / nuclear estrogen receptor binding / hippocampus development / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Heme signaling / SUMOylation of intracellular receptors / euchromatin / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / male gonad development / Circadian Clock / response to estradiol / HATs acetylate histones / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / cellular response to lipopolysaccharide / transcription regulator complex / sequence-specific DNA binding / transcription by RNA polymerase II / transcription coactivator activity
Similarity search - Function
Bile acid receptor, ligand binding domain / Thyroid hormone receptor / Nuclear receptor coactivator 1 / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain ...Bile acid receptor, ligand binding domain / Thyroid hormone receptor / Nuclear receptor coactivator 1 / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / Nuclear receptor coactivator, interlocking / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-9KV / Nuclear receptor coactivator / Nuclear receptor coactivator 1 / Bile acid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
Model detailsStructures re-refined for D3R docking challenge
AuthorsRudolph, M.G. / Benz, J. / Burger, D. / Thoma, R. / Ruf, A. / Joseph, C. / Kuhn, B. / Shao, C. / Yang, H. / Burley, S.K.
CitationJournal: J. Comput. Aided Mol. Des. / Year: 2018
Title: D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.
Authors: Gaieb, Z. / Liu, S. / Gathiaka, S. / Chiu, M. / Yang, H. / Shao, C. / Feher, V.A. / Walters, W.P. / Kuhn, B. / Rudolph, M.G. / Burley, S.K. / Gilson, M.K. / Amaro, R.E.
History
DepositionMay 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Feb 21, 2018Group: Structure summary / Category: pdbx_deposit_group / Item: _pdbx_deposit_group.group_type
Revision 1.5Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.identifier_ORCID / _citation.country / _citation_author.identifier_ORCID
Revision 1.6Nov 17, 2021Group: Database references / Structure summary / Category: database_2 / pdbx_deposit_group
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_deposit_group.group_description

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bile acid receptor
B: COACTIVATOR PEPTIDE SRC-1 HD3
C: Bile acid receptor
D: COACTIVATOR PEPTIDE SRC-1 HD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7766
Polymers57,7804
Non-polymers9952
Water4,017223
1
A: Bile acid receptor
B: COACTIVATOR PEPTIDE SRC-1 HD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3883
Polymers28,8902
Non-polymers4981
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-6 kcal/mol
Surface area11970 Å2
MethodPISA
2
C: Bile acid receptor
D: COACTIVATOR PEPTIDE SRC-1 HD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3883
Polymers28,8902
Non-polymers4981
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-8 kcal/mol
Surface area11850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.865, 84.076, 188.931
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and resid 746 through 755)
21chain D
12(chain A and (resid 248 through 331 or resid 333...
22(chain C and (resid 248 through 331 or resid 333...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain B and resid 746 through 755)B746 - 755
211chain DD746 - 755
112(chain A and (resid 248 through 331 or resid 333...A248 - 331
122(chain A and (resid 248 through 331 or resid 333...A333 - 352
132(chain A and (resid 248 through 331 or resid 333...A354 - 357
142(chain A and (resid 248 through 331 or resid 333...A359 - 374
152(chain A and (resid 248 through 331 or resid 333...A376 - 395
162(chain A and (resid 248 through 331 or resid 333...A397 - 404
172(chain A and (resid 248 through 331 or resid 333...A406 - 412
182(chain A and (resid 248 through 331 or resid 333...A414 - 425
192(chain A and (resid 248 through 331 or resid 333...A427 - 435
1102(chain A and (resid 248 through 331 or resid 333...A437 - 442
1112(chain A and (resid 248 through 331 or resid 333...A444 - 452
1122(chain A and (resid 248 through 331 or resid 333...A455 - 458
1132(chain A and (resid 248 through 331 or resid 333...A460 - 476
212(chain C and (resid 248 through 331 or resid 333...C248 - 331
222(chain C and (resid 248 through 331 or resid 333...C333 - 352
232(chain C and (resid 248 through 331 or resid 333...C354 - 357
242(chain C and (resid 248 through 331 or resid 333...C359 - 374
252(chain C and (resid 248 through 331 or resid 333...C376 - 395
262(chain C and (resid 248 through 331 or resid 333...C397 - 404
272(chain C and (resid 248 through 331 or resid 333...C406 - 412
282(chain C and (resid 248 through 331 or resid 333...C414 - 425
292(chain C and (resid 248 through 331 or resid 333...C427 - 435
2102(chain C and (resid 248 through 331 or resid 333...C437 - 442
2112(chain C and (resid 248 through 331 or resid 333...C444 - 452
2122(chain C and (resid 248 through 331 or resid 333...C455 - 458
2132(chain C and (resid 248 through 331 or resid 333...C460 - 476

NCS ensembles :
ID
1
2

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Components

#1: Protein Bile acid receptor / Farnesoid X-activated receptor / Farnesol receptor HRR-1 / Nuclear receptor subfamily 1 group H ...Farnesoid X-activated receptor / Farnesol receptor HRR-1 / Nuclear receptor subfamily 1 group H member 4 / Retinoid X receptor-interacting protein 14 / RXR-interacting protein 14


Mass: 27100.191 Da / Num. of mol.: 2 / Fragment: UNP residues 258-486
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1H4, BAR, FXR, HRR1, RIP14 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / References: UniProt: Q96RI1
#2: Protein/peptide COACTIVATOR PEPTIDE SRC-1 HD3


Mass: 1790.026 Da / Num. of mol.: 2 / Fragment: UNP residues 744-757 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: A8K1V4, UniProt: Q15788*PLUS
#3: Chemical ChemComp-9KV / (2S)-N,2-dicyclohexyl-2-[2-(5-phenylthiophen-2-yl)-1H-benzimidazol-1-yl]acetamide


Mass: 497.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H35N3OS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 298 K / Method: evaporation, hanging drop / pH: 6.5
Details: 0.2 M Na Chloride, 0.1 M Bis-Tris pH 6.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 27, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→38.4 Å / Num. all: 39139 / Num. obs: 38634 / % possible obs: 98.7 % / Redundancy: 0.99 % / Net I/σ(I): 13.46
Reflection shellResolution: 2→2.1 Å / Redundancy: 1 % / Num. possible: 5247 / Num. unique obs: 5241 / Net I/σ(I) obs: 2.24 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.23data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→35.729 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2471 1922 4.99 %
Rwork0.1945 36578 -
obs0.1972 38500 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.66 Å2 / Biso mean: 46.0839 Å2 / Biso min: 17.11 Å2
Refinement stepCycle: final / Resolution: 2→35.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3949 0 83 223 4255
Biso mean--33.55 49.5 -
Num. residues----481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014231
X-RAY DIFFRACTIONf_angle_d1.3245739
X-RAY DIFFRACTIONf_chiral_restr0.062635
X-RAY DIFFRACTIONf_plane_restr0.009733
X-RAY DIFFRACTIONf_dihedral_angle_d10.0853543
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B78X-RAY DIFFRACTION10.7TORSIONAL
12D78X-RAY DIFFRACTION10.7TORSIONAL
21A1962X-RAY DIFFRACTION10.7TORSIONAL
22C1962X-RAY DIFFRACTION10.7TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.32461410.273726442785100
2.05-2.10540.31861400.263525822722100
2.1054-2.16740.28271360.245325852721100
2.1674-2.23730.4051230.34852421254492
2.2373-2.31730.41741170.32672339245688
2.3173-2.410.26031370.215626442781100
2.41-2.51970.25921270.20726332760100
2.5197-2.65250.26541410.226262767100
2.6525-2.81860.26411420.202126302772100
2.8186-3.03620.25871310.205626552786100
3.0362-3.34150.2691250.196826672792100
3.3415-3.82450.25121430.181426772820100
3.8245-4.81660.20181660.149726762842100
4.8166-35.73510.19981530.165727992952100
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)
10.7406-0.5149-0.26320.5650.51880.7667-0.0996-0.1943-0.2657-0.1395-0.03280.55140.5077-0.4938-0.16190.251-0.1778-0.06530.34630.01850.373-2.547115.1356-16.4717
20.50740.0599-0.34240.1344-0.08130.23180.1045-0.36570.10220.3341-0.1380.14570.3377-0.32450.00150.2445-0.08170.02630.2866-0.06630.276110.289917.48545.7683
30.12320.04680.02940.3727-0.53890.8092-0.0317-0.07610.0168-0.1114-0.1711-0.07980.14780.064300.2381-0.00570.01980.19550.0030.284713.811113.8799-9.9826
4-0.0009-0.00050.00580.5352-0.46070.43820.00230.11410.22190.3003-0.2643-0.0702-0.4901-0.31-0.05060.3580.10290.00060.4228-0.14960.41168.90932.44847.5425
50.1217-0.0603-0.07580.07810.08650.09550.2122-0.18250.19920.12840.06570.0994-0.40230.14140.00470.3436-0.08-0.0670.27880.05090.454115.599533.1139-2.8838
60.25580.32660.13420.5041-0.02190.34-0.14050.34650.4239-0.07460.0787-0.24740.13910.1239-0.00070.22120.02030.01360.2506-0.00170.261112.09718.4535-14.9687
70.2797-0.0480.14660.1819-0.18550.371-0.20860.05840.4328-0.56120.02820.06870.0526-0.01250.0030.3691-0.0121-0.05120.27120.00540.39386.091122.8649-22.5603
80.071-0.1005-0.04010.13550.11910.1191-0.2303-0.02830.4450.0318-0.1563-0.2318-0.24540.2226-0.00570.3235-0.0279-0.06060.36120.02870.507918.735626.3252-9.4614
90.0456-0.09160.0040.25140.03930.1313-0.0721-0.28080.3624-0.2861-0.0757-0.23450.2816-0.13540.00460.3347-0.036-0.08510.3144-0.03880.442725.454219.496810.267
100.0366-0.01460.03440.02140.01180.08560.25630.01120.06830.0886-0.024-0.26020.27920.53450.00260.3320.00380.05860.27440.0560.460423.807911.67840.3523
110.0373-0.11440.13660.3641-0.38280.54580.35890.1209-0.2602-0.0281-0.2425-0.53130.80040.1632-0.00030.3723-0.0523-0.00780.22630.03150.337619.041.3756-5.5741
120.06610.02820.03290.2019-0.0220.1358-0.05040.0204-0.14060.10390.2051-0.03780.06590.3683-0.00020.4670.1810.02210.3632-0.02720.352830.767339.661927.0667
130.27120.1719-0.17620.3364-0.13740.3621-0.3188-0.7591-0.23510.70860.1024-0.18360.31180.5528-0.00480.48650.18820.08120.50080.06720.249419.193751.227646.965
140.0417-0.02170.02550.20080.25340.6115-0.2401-0.1072-0.00080.22070.135-0.10160.07320.228800.2930.09360.02510.37110.00640.28427.162355.897533.192
150.03470.0679-0.08530.1329-0.15660.1672-0.1018-0.0933-0.1259-0.0316-0.1382-0.02850.3716-0.0501-2.16230.29490.14260.57910.2234-0.09120.00854.953147.505843.9073
160.43340.1930.40450.43620.08480.4962-0.135-0.05540.2240.0960.04870.00950.1876-0.2347-00.2630.04930.05020.3437-0.00570.255917.385853.579629.7431
170.2113-0.1310.05870.1539-0.10930.3754-0.25590.3622-0.0087-0.54620.16190.18350.06310.1004-0.00180.34140.03990.04210.3237-0.0120.307624.319446.845318.6787
180.1852-0.0712-0.07150.06840.00780.0704-0.0504-0.03420.0925-0.1574-0.03160.0857-0.1966-0.1426-0.0010.34920.09980.02570.3440.01240.279814.148458.609729.5255
190.0861-0.10740.10050.2398-0.19220.1546-0.1091-0.13270.41410.7343-0.26620.2683-0.27920.1002-0.02440.45540.09830.04190.6121-0.08280.445312.284265.338149.9745
200.2108-0.1771-0.08010.19670.05660.06820.5258-0.00010.2098-0.59230.5662-0.1309-0.27390.36550.00490.49950.0279-0.01970.7144-0.03020.358823.955665.87243.5728
211.84760.3204-0.44180.5179-0.42160.3683-0.0231-0.04710.425-0.08260.03780.0743-0.61170.29970.05860.43910.0426-0.14530.7652-0.02680.349337.10261.702341.2231
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 247 through 266 )A247 - 266
2X-RAY DIFFRACTION2chain 'A' and (resid 267 through 307 )A267 - 307
3X-RAY DIFFRACTION3chain 'A' and (resid 308 through 341 )A308 - 341
4X-RAY DIFFRACTION4chain 'A' and (resid 342 through 362 )A342 - 362
5X-RAY DIFFRACTION5chain 'A' and (resid 363 through 379 )A363 - 379
6X-RAY DIFFRACTION6chain 'A' and (resid 380 through 404 )A380 - 404
7X-RAY DIFFRACTION7chain 'A' and (resid 405 through 432 )A405 - 432
8X-RAY DIFFRACTION8chain 'A' and (resid 433 through 456 )A433 - 456
9X-RAY DIFFRACTION9chain 'A' and (resid 457 through 466 )A457 - 466
10X-RAY DIFFRACTION10chain 'A' and (resid 467 through 476 )A467 - 476
11X-RAY DIFFRACTION11chain 'B' and (resid 745 through 755 )B745 - 755
12X-RAY DIFFRACTION12chain 'C' and (resid 247 through 266 )C247 - 266
13X-RAY DIFFRACTION13chain 'C' and (resid 267 through 307 )C267 - 307
14X-RAY DIFFRACTION14chain 'C' and (resid 308 through 341 )C308 - 341
15X-RAY DIFFRACTION15chain 'C' and (resid 342 through 362 )C342 - 362
16X-RAY DIFFRACTION16chain 'C' and (resid 363 through 404 )C363 - 404
17X-RAY DIFFRACTION17chain 'C' and (resid 405 through 432 )C405 - 432
18X-RAY DIFFRACTION18chain 'C' and (resid 433 through 456 )C433 - 456
19X-RAY DIFFRACTION19chain 'C' and (resid 457 through 466 )C457 - 466
20X-RAY DIFFRACTION20chain 'C' and (resid 467 through 476 )C467 - 476
21X-RAY DIFFRACTION21chain 'D' and (resid 746 through 755 )D746 - 755

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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

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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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