9GES | pdb_00009ges

Crystal structure of HEI10

PDB DOI: https://doi.org/10.2210/pdb9GES/pdb

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

Deposited: 2024-08-07 Released: 2025-08-20
Deposition Author(s): Milburn, A.E., Espejo-Serrano, C., Dunce, J.M., Davies, O.R.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.43 Å
R-Value Free:
0.289 (Depositor), 0.288 (DCC)
R-Value Work:
0.250 (Depositor), 0.249 (DCC)
R-Value Observed:
0.252 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9GES

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of HEI10

Milburn, A.E., Espejo-Serrano, C., Dunce, J.M., Davies, O.R.

To be published.

Macromolecule Content

Total Structure Weight: 91.9 kDa
Atom Count: 5,800
Modeled Residue Count: 712
Deposited Residue Count: 792
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase CCNB1IP1	A, B, C, D	198	Homo sapiens	Mutation(s): 0 Gene Names: CCNB1IP1, C14orf18, HEI10 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPC3 (Homo sapiens) Explore Q9NPC3 Go to UniProtKB: Q9NPC3
PHAROS: Q9NPC3 GTEx: ENSG00000100814
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NPC3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain K [auth D] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C] mmCIF format, chain K [auth D] mmCIF format, chain L [auth D]	E [auth A] F [auth A] G [auth B] H [auth B] I [auth C] E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], K [auth D], L [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.43 Å
R-Value Free: 0.289 (Depositor), 0.288 (DCC)
R-Value Work: 0.250 (Depositor), 0.249 (DCC)
R-Value Observed: 0.252 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.198	α = 90
b = 73.857	β = 99.276
c = 124.032	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-08-20

Deposition Author(s):

Espejo-Serrano, C.

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	219413/Z/19/Z

Revision History (Full details and data files)

Version 1.0: 2025-08-20
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.