9IIC | pdb_00009iic

Crystal structure of HOIP RING2-LDD in complex with STK4 KD domain

  • Classification: LIGASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2024-06-20 Released: 2025-06-25 
  • Deposition Author(s): Wang, Y.R., Zhou, X.D., Pan, L.F.
  • Funding Organization(s): National Basic Research Program of China (973 Program), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 
    0.280 (Depositor), 0.279 (DCC) 
  • R-Value Work: 
    0.237 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.239 (Depositor) 

Starting Models: experimental
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Literature

Crystal structure of HOIP RING2-LDD in complex with STK4 KD domain

Wang, Y.R., Zhou, X.D., Pan, L.F.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase 4 37kDa subunitA [auth B],
C [auth A]		302Homo sapiensMutation(s): 1 
Gene Names: STK4, KRS2, MST1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13043 (Homo sapiens)
Explore Q13043 
Go to UniProtKB:  Q13043
PHAROS:  Q13043
GTEx:  ENSG00000101109 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13043
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RNF31B [auth C],
D		215Homo sapiensMutation(s): 0 
Gene Names: RNF31, ZIBRA
EC: 2.3.2.31
UniProt & NIH Common Fund Data Resources
Find proteins for Q96EP0 (Homo sapiens)
Explore Q96EP0 
Go to UniProtKB:  Q96EP0
PHAROS:  Q96EP0
GTEx:  ENSG00000092098 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96EP0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL (Subject of Investigation/LOI)
Query on GOL
Download Ideal Coordinates CCD File 
E [auth B],
J [auth A]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN
Download Ideal Coordinates CCD File 
F [auth C]
G [auth C]
H [auth C]
I [auth C]
K [auth D]
F [auth C],
G [auth C],
H [auth C],
I [auth C],
K [auth D],
L [auth D],
M [auth D],
N [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free:  0.280 (Depositor), 0.279 (DCC) 
  • R-Value Work:  0.237 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.239 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.989α = 90
b = 96.363β = 118.82
c = 115.773γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Basic Research Program of China (973 Program)China2022YFC2303102
National Natural Science Foundation of China (NSFC)China32071219
National Natural Science Foundation of China (NSFC)China92253301
National Natural Science Foundation of China (NSFC)China21822705
National Natural Science Foundation of China (NSFC)China32071297

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-25
    Type: Initial release