3ZW5 | pdb_00003zw5

Crystal structure of the human Glyoxalase domain-containing protein 5

• PDB DOI: https://doi.org/10.2210/pdb3ZW5/pdb

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


• Deposited: 2011-07-28 Released: 2011-08-10 
• Deposition Author(s): Muniz, J.R.C., Kiyani, W., Froese, S., Vollmar, M., von Delft, F., Burgess-Brown, N., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Yue, W.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.199 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Literature

Crystal Structure of the Human Glyoxalase Domain-Containing Protein 5

Muniz, J.R.C., Kiyani, W., Vollmar, M., von Delft, F., Burgess-Brown, N., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Yue, W.W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.11 kDa 
• Atom Count: 2,298 
• Modelled Residue Count: 255 
• Deposited Residue Count: 294 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYOXALASE DOMAIN-CONTAINING PROTEIN 5	A, B	147	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for A6NK44 (Homo sapiens) Explore A6NK44  Go to UniProtKB:  A6NK44
PHAROS:  A6NK44 GTEx:  ENSG00000171433

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	C [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	E [auth A], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.199 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.49	α = 90
b = 66.04	β = 90
c = 76.87	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-10 
Deposition Author(s): Muniz, J.R.C., Kiyani, W., Froese, S., Vollmar, M., von Delft, F., Burgess-Brown, N., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Yue, W.W.

Revision History  

• Version 1.0: 2011-08-10
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other