5JNO

Crystal structure of the BD1-NTPR complex from BEND3 and PICH

> Summary

Summary for 5JNO

DescriptorBEN domain-containing protein 3, DNA excision repair protein ERCC-6-like, GLYCEROL, ... (4 entities in total)
Functional Keywordsultra fine chromatin bridges, sister chromatids separation, anaphase, cell cycle
Biological sourceHomo sapiens (Human)
Cellular locationNucleus  Q5T5X7
Chromosome, centromere Q2NKX8
Total number of polymer chains2
Total molecular weight19474.13
Authors
Pitchai, G.,Mesa, P.,Hickson, I.D.,Montoya, G. (deposition date: 2016-04-30, release date: 2017-09-13)
Primary citation
Pitchai, G.,Mesa, P.,Hickson, I.D.,Montoya, G.
Crystal structure of the BD1-NTPR complex from BEND3 and PICH
To Be Published,
Experimental method
X-RAY DIFFRACTION (2.2 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.24332.7%5.2%2.6%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

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

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
ABEN domain-containing protein 3polymer11212866.71
UniProt (Q5T5X7)
Pfam (PF10523)
Homo sapiens (Human)BEND3
BDNA excision repair protein ERCC-6-likepolymer576515.41
UniProt (Q2NKX8)
Homo sapiens (Human)ATP-dependent helicase ERCC6-like,PLK1-interacting checkpoint helicase,Tumor antigen BJ-HCC-15
GLYCEROLnon-polymer92.11
waterwater18.018

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight19382.0
Non-Polymers*Number of molecules1
Total molecular weight92.1
All*Total molecular weight19474.1
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.2 Å)

Cell axes47.28047.280431.579
Cell angles90.0090.00120.00
SpacegroupP 61 2 2
Resolution limits71.93 - 2.20
the highest resolution shell value2.254 - 2.197
R-factor0.22236
R-work0.22151
the highest resolution shell value0.310
R-free0.23748
the highest resolution shell value0.304
RMSD bond length0.013
RMSD bond angle1.587

Data Collection Statistics

Resolution limits71.93 - 2.20
the highest resolution shell value -
Number of reflections14907
Completeness99.1
Redundancy20

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, SITTING DROP293

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 GOL A 401
ChainResidue
ASER301
AGLN305
AARG308
ATRP324

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

site_idNumber of ResiduesDetails
GOL_5jno_A_4016GLYCEROL binding site
ChainResidueligand
ASER301GOL: GLYCEROL
ALEU304-GLN305GOL: GLYCEROL
AARG308GOL: GLYCEROL
ATRP324GOL: GLYCEROL
ALEU329GOL: GLYCEROL

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI18ATP. {ECO:0000305}.
ChainResidueDetails
BNA*

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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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