9CSJ | pdb_00009csj

Crystal structure of human glyoxalase domain-containing protein 4 (GLOD4) at 2.33 A resolution.

PDB DOI: https://doi.org/10.2210/pdb9CSJ/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-07-24 Released: 2025-08-13
Deposition Author(s): Griswold-Prenner, I., Dou, Y., Jennings, A., Kayser, F.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free:
0.269 (Depositor), 0.275 (DCC)
R-Value Work:
0.220 (Depositor), 0.225 (DCC)
R-Value Observed:
0.223 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of apo-Glyoxalase domain-containing protein 4 (apo-GLOD4) at 2.33 A resolution.

Griswold-Prenner, I., Kayser, F.

To be published.

Macromolecule Content

Total Structure Weight: 101.6 kDa
Atom Count: 7,425
Modeled Residue Count: 868
Deposited Residue Count: 897
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Glyoxalase domain-containing protein 4	A, B, C	299	Homo sapiens	Mutation(s): 0 Gene Names: GLOD4, C17orf25, CGI-150, My027
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HC38 (Homo sapiens) Explore Q9HC38 Go to UniProtKB: Q9HC38
PHAROS: Q9HC38 GTEx: ENSG00000167699
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HC38
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain Y [auth C] MOL2 format, chain R [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain R [auth B] mmCIF format, chain Y [auth C]	R [auth B], Y [auth C]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain R [auth B] Focus chain Y [auth C] Interactions & Density Focus chain R [auth B] Focus chain Y [auth C]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain X [auth B] MOL2 format, chain O [auth A] MOL2 format, chain X [auth B] mmCIF format, chain O [auth A] mmCIF format, chain X [auth B]	O [auth A], X [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain X [auth B] Interactions & Density Focus chain O [auth A] Focus chain X [auth B]
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 A] SDF format, chain S [auth B] SDF format, chain Z [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain S [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain S [auth B] mmCIF format, chain Z [auth C]	E [auth A], F [auth A], G [auth A], S [auth B], Z [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain S [auth B] Focus chain Z [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain S [auth B] Focus chain Z [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B]	AA [auth C] H [auth A] I [auth A] J [auth A] K [auth A] AA [auth C], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], T [auth B], U [auth B], V [auth B], W [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain AA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain D [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain D [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B]	D [auth A], P [auth B], Q [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain D [auth A] Focus chain P [auth B] Focus chain Q [auth B]