5POJ

PanDDA analysis group deposition -- Crystal Structure of BRD1 in complex with N10941a

> Summary

Summary for 5POJ

Group depositionPanDDA analysis group deposition (G_1002022)
Functional Keywordspandda, sgc - diamond i04-1 fragment screening, bromodomain, epigenetics, xchemexplorer, gene regulation
Biological sourceHomo sapiens (Human)
Cellular locationNucleus  O95696
Total number of polymer chains2
Total molecular weight37123.2
Authors
Primary citation
Pearce, N.M.,Krojer, T.,Bradley, A.R.,Collins, P.,Nowak, R.,Talon, R.,Marsden, B.,Kelm, S.,Shi, J.,Deane, D.,von Delft, F.
A Multi-Crystal Method for Extracting Obscured Crystallographic States from Conventionally Uninterpretable Electron Density
Nat Commun, 2017
Experimental method
X-RAY DIFFRACTION (1.62 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.236300.5%2.4%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5poj
no rotation
Molmil generated image of 5poj
rotated about x axis by 90°
Molmil generated image of 5poj
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 5poj
no rotation
Molmil generated image of 5poj
rotated about x axis by 90°
Molmil generated image of 5poj
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (5poj.pdb1.gz [25 KB])
Coordinate files for Biological unit (5poj.pdb2.gz [27.44 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, BBromodomain-containing protein 1polymer15618224.72
UniProt (O95696)
Pfam (PF00439)
Homo sapiens (Human)BR140-like protein,Bromodomain and PHD finger-containing protein 2
1,2-ETHANEDIOLnon-polymer62.13
N-(1-benzylpiperidin-4-yl)acetamidenon-polymer232.32
SODIUM IONnon-polymer23.01
waterwater18.0269

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight36449.4
Non-Polymers*Number of molecules6
Total molecular weight673.8
All*Total molecular weight37123.2
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.62 Å)

Cell axes55.71656.384101.685
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits21.67 - 1.62
the highest resolution shell value1.661 - 1.620
R-factor0.1987
R-work0.19680
the highest resolution shell value0.294
R-free0.23620
the highest resolution shell value0.300
RMSD bond length0.007
RMSD bond angle1.064

Data Collection Statistics

Resolution limits21.67 - 1.62
the highest resolution shell value -
Number of reflections40527
Rmerge_l_obs0.134
the highest resolution shell value0.667
Completeness97.8
Redundancy5.4
the highest resolution shell value5

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, SITTING DROP7293

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC14binding site for residue EDO A 201
ChainResidue
ATYR109
AASN110
AEDO202
A8RV203

AC28binding site for residue EDO A 202
ChainResidue
AILE54
APHE55
ACYS106
AEDO201
A8RV203
AHOH305
AHOH312
AHOH313

AC314binding site for residue 8RV A 203
ChainResidue
AVAL59
AGLU63
AVAL64
AASN110
APHE116
AEDO201
AEDO202
AHOH305
AHOH313
AHOH379
AHOH387
BSER22
BMET23
BVAL26

AC46binding site for residue NA B 201
ChainResidue
ALYS108
AHOH361
BMET107
BASN110
BTYR117
BHOH341

AC55binding site for residue EDO B 202
ChainResidue
BLEU92
BGLU96
BLEU131
BARG135
BHOH376

AC67binding site for residue 8RV B 203
ChainResidue
AGLU63
BGLU63
BTYR109
BASN110
BPHE116
BHOH316
BHOH337

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
EDO_5poj_A_20291,2-ETHANEDIOL binding site
ChainResidueligand
AILE54-PHE55EDO: 1,2-ETHANEDIOL
AVAL59EDO: 1,2-ETHANEDIOL
ATYR67EDO: 1,2-ETHANEDIOL
AILE102EDO: 1,2-ETHANEDIOL
AASN105-CYS106EDO: 1,2-ETHANEDIOL
AASN110EDO: 1,2-ETHANEDIOL
APHE116EDO: 1,2-ETHANEDIOL

8RV_5poj_A_20310N-(1-benzylpiperidin-4-yl)acetamide binding site
ChainResidueligand
AILE54-PHE558RV: N-(1-benzylpiperidin-4-yl)acetamide
AVAL598RV: N-(1-benzylpiperidin-4-yl)acetamide
AGLU63-VAL648RV: N-(1-benzylpiperidin-4-yl)acetamide
ATYR678RV: N-(1-benzylpiperidin-4-yl)acetamide
ACYS1068RV: N-(1-benzylpiperidin-4-yl)acetamide
ATYR109-ASN1108RV: N-(1-benzylpiperidin-4-yl)acetamide
APHE1168RV: N-(1-benzylpiperidin-4-yl)acetamide

EDO_5poj_A_20161,2-ETHANEDIOL binding site
ChainResidueligand
AVAL59EDO: 1,2-ETHANEDIOL
ATYR67EDO: 1,2-ETHANEDIOL
ATYR109-ASN110EDO: 1,2-ETHANEDIOL
APHE116EDO: 1,2-ETHANEDIOL
BARG112EDO: 1,2-ETHANEDIOL

8RV_5poj_B_20312N-(1-benzylpiperidin-4-yl)acetamide binding site
ChainResidueligand
BILE54-PHE558RV: N-(1-benzylpiperidin-4-yl)acetamide
BVAL598RV: N-(1-benzylpiperidin-4-yl)acetamide
BGLU63-TYR678RV: N-(1-benzylpiperidin-4-yl)acetamide
BCYS1068RV: N-(1-benzylpiperidin-4-yl)acetamide
BTYR109-ASN1108RV: N-(1-benzylpiperidin-4-yl)acetamide
BPHE1168RV: N-(1-benzylpiperidin-4-yl)acetamide

EDO_5poj_B_20261,2-ETHANEDIOL binding site
ChainResidueligand
BLEU92-HIS93EDO: 1,2-ETHANEDIOL
BGLU96EDO: 1,2-ETHANEDIOL
BLEU131-ARG132EDO: 1,2-ETHANEDIOL
BARG135EDO: 1,2-ETHANEDIOL

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
PS006332
ChainResidueDetails
AALA52-TYR109
BALA52-TYR109

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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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