8W5A | pdb_00008w5a

Crystal structure of the RING domain of human XIAP

• PDB DOI: https://doi.org/10.2210/pdb8W5A/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-08-25 Released: 2023-09-27 
• Deposition Author(s): Zhang, Q., Sun, H., Hu, X., Wang, M.
• Funding Organization(s): The University Grants Committee, Research Grants Council (RGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the RING domain of human XIAP

Zhang, Q., Sun, H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 15.15 kDa 
• Atom Count: 1,038 
• Modeled Residue Count: 126 
• Deposited Residue Count: 128 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase XIAP	A, B	64	Homo sapiens	Mutation(s): 0  Gene Names: XIAP, API3, BIRC4, IAP3 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for P98170 (Homo sapiens) Explore P98170  Go to UniProtKB:  P98170
PHAROS:  P98170 GTEx:  ENSG00000101966

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	C [auth A], D [auth A], F [auth B], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	E [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.696	α = 90
b = 48.742	β = 97.28
c = 39.639	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-27 
Deposition Author(s): Zhang, Q., Sun, H., Hu, X., Wang, M.

---

Funding Organization	Location	Grant Number
The University Grants Committee, Research Grants Council (RGC)	Hong Kong	R7070-18

Revision History  

• Version 1.0: 2023-09-27
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Structure summary
• Version 1.2: 2023-10-25
  Changes: Structure summary