5ZBU

Crystal Structure of PA-TM-RING E3 ligase RNF13 RING domain in complex with E2~Ub


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


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Literature

Crystal Structure of PA-TM-RING E3 ligase RNF13 RING domain in complex with E2~Ub

Sarkar, S.Datta, A.B.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 D2B,
A [auth C]
148Homo sapiensMutation(s): 1 
Gene Names: UBE2D2PUBC1UBC4UBC5BUBCH4UBCH5B
EC: 2.3.2.23 (PDB Primary Data), 2.3.2.24 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P62837 (Homo sapiens)
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Go to UniProtKB:  P62837
PHAROS:  P62837
GTEx:  ENSG00000131508 
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UniProt GroupP62837
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RNF13C [auth A],
D
76Homo sapiensMutation(s): 0 
Gene Names: RNF13RZF
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for O43567 (Homo sapiens)
Explore O43567 
Go to UniProtKB:  O43567
PHAROS:  O43567
GTEx:  ENSG00000082996 
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UniProt GroupO43567
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinE76Homo sapiensMutation(s): 0 
Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
PHAROS:  P0CG47
Entity Groups  
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UniProt GroupP0CG47
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.559α = 90
b = 105.74β = 115.49
c = 60.79γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome Trust-DBT India AllianceIndia500241/Z/11/Z

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release