7CJB

VHL recognizes hydroxyproline in RIPK1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

VHL recognizes hydroxyproline in RIPK1

Liu, J.Wang, Y.Pan, L.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
von Hippel-Lindau disease tumor suppressor
A, E, I, M
163Homo sapiensMutation(s): 0 
Gene Names: VHL
UniProt & NIH Common Fund Data Resources
Find proteins for P40337 (Homo sapiens)
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Go to UniProtKB:  P40337
PHAROS:  P40337
GTEx:  ENSG00000134086 
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UniProt GroupP40337
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-B
B, F, J, N
122Homo sapiensMutation(s): 0 
Gene Names: ELOBTCEB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens)
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PHAROS:  Q15370
GTEx:  ENSG00000103363 
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UniProt GroupQ15370
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-C
C, G, K, O
100Homo sapiensMutation(s): 0 
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PHAROS:  Q15369
GTEx:  ENSG00000154582 
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UniProt GroupQ15369
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  • Reference Sequence

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
THR-LEU-TYR-TYR-MET-ALA-PRO-GLU-HIS-LEU-ASN-ASP-VAL-ASN-ALA
D, H, L, P
15Homo sapiensMutation(s): 0 
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13546 (Homo sapiens)
Explore Q13546 
Go to UniProtKB:  Q13546
PHAROS:  Q13546
GTEx:  ENSG00000137275 
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UniProt GroupQ13546
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HYP
Query on HYP
D, H, L, P
L-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.831α = 90
b = 94.831β = 90
c = 361.605γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31500597
National Natural Science Foundation of China (NSFC)China21621002

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-14
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description