4O2W

Crystal structure of the third RCC1-like domain of HERC1

• PDB DOI: https://doi.org/10.2210/pdb4O2W/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-12-17 Released: 2014-01-15 
• Deposition Author(s): Dong, A., Hu, J., Li, Y., Walker, J.R., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Tong, Y., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.221 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 

Starting Model: experimental

Literature

Crystal structure of the third RCC1-like domain of HERC1

Hu, J., Dong, A., Li, Y., Walker, J.R., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Tong, Y., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 171.95 kDa 
• Atom Count: 11,463 
• Modelled Residue Count: 1,459 
• Deposited Residue Count: 1,616 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase HERC1	A, B, C, D	404	Homo sapiens	Mutation(s): 0  Gene Names: HERC1 EC: 6.3.2 (PDB Primary Data), 2.3.2.26 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q15751 (Homo sapiens) Explore Q15751  Go to UniProtKB:  Q15751
PHAROS:  Q15751 GTEx:  ENSG00000103657

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	BA [auth D], CA [auth D], F [auth A], G [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	AA [auth D], E [auth A], N [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNX	DA [auth D], EA [auth D], FA [auth D], GA [auth D], HA [auth D], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], KA [auth D], L [auth A], M [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth C], Y [auth C], Z [auth C]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.221 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.383	α = 70.93
b = 70.902	β = 81.26
c = 105.549	γ = 90.84

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-15 
Deposition Author(s): Dong, A., Hu, J., Li, Y., Walker, J.R., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Tong, Y., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2014-01-15
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description