3ZI1 | pdb_00003zi1

Crystal structure of human glyoxalase domain-containing protein 4 (GLOD4)

• PDB DOI: https://doi.org/10.2210/pdb3ZI1/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-12-30 Released: 2013-01-16 
• Deposition Author(s): Oberholzer, A., Kiyani, W., Shrestha, L., Vollmar, M., Krojer, T., Froese, D.S., Williams, E., von Delft, F., Burgess-Brown, N., Arrowsmith, C.H., Edwards, A., Bountra, C., Yue, W.W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.204 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Human Glyoxalase Domain- Containing Protein 4 (Glod4)

Oberholze, A., Kiyani, W., Shrestha, L., Vollmar, M., Krojer, T., Froese, D.S., Williams, E., von Delft, F., Burgess-Brown, N., Arrowsmith, C.H., Edwards, A., Bountra, C., Yue, W.W.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 37.16 kDa 
• Atom Count: 2,567 
• Modeled Residue Count: 274 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYOXALASE DOMAIN-CONTAINING PROTEIN 4	A	330	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HC38 (Homo sapiens) Explore Q9HC38  Go to UniProtKB:  Q9HC38
PHAROS:  Q9HC38 GTEx:  ENSG00000167699

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.204 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.291	α = 90
b = 42.918	β = 90
c = 68.103	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-16 
Deposition Author(s): Oberholzer, A., Kiyani, W., Shrestha, L., Vollmar, M., Krojer, T., Froese, D.S., Williams, E., von Delft, F., Burgess-Brown, N., Arrowsmith, C.H., Edwards, A., Bountra, C., Yue, W.W.

Revision History  

• Version 1.0: 2013-01-16
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description