6GMC | pdb_00006gmc

1.2 A resolution structure of human hydroxyacid oxidase 1 bound with FMN and 4-carboxy-5-[(4-chlorophenyl)sulfanyl]-1,2,3-thiadiazole

• PDB DOI: https://doi.org/10.2210/pdb6GMC/pdb

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


• Deposited: 2018-05-24 Released: 2018-06-13 
• Deposition Author(s): MacKinnon, S., Bezerra, G.A., Krojer, T., Smee, C., Arrowsmith, C.H., Edwards, E., Bountra, C., Oppermann, U., Brennan, P.E., Yue, W.W.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.155 (Depositor), 0.162 (DCC) 
• R-Value Work: 
  0.134 (Depositor), 0.143 (DCC) 
• R-Value Observed: 
  0.135 (Depositor) 

Starting Model: experimental

Literature

Structure of human hydroxyacid oxidase 1 bound with FMN and glycolate

MacKinnon, S., Bezerra, G.A., Krojer, T., Smee, C., Arrowsmith, C.H., Edwards, E., Bountra, C., Oppermann, U., Brennan, P.E., Yue, W.W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 41.71 kDa 
• Atom Count: 3,277 
• Modeled Residue Count: 360 
• Deposited Residue Count: 368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxyacid oxidase 1	A	368	Homo sapiens	Mutation(s): 0  Gene Names: HAO1, GOX1, HAOX1 EC: 1.1.3.15 (PDB Primary Data), 1.2.3.5 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJM8 (Homo sapiens) Explore Q9UJM8  Go to UniProtKB:  Q9UJM8
PHAROS:  Q9UJM8 GTEx:  ENSG00000101323

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	F [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
C7C	G [auth A]	5-[(4-chlorophenyl)sulfanyl]-1,2,3-thiadiazole-4-carboxylate C9 H4 Cl N2 O2 S2 NDYKFFAREALEPX-UHFFFAOYSA-M
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: 1.20 Å
• R-Value Free:  0.155 (Depositor), 0.162 (DCC) 
• R-Value Work:  0.134 (Depositor), 0.143 (DCC) 
• R-Value Observed: 0.135 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.348	α = 90
b = 97.348	β = 90
c = 80.363	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-06-13 
Deposition Author(s): MacKinnon, S., Bezerra, G.A., Krojer, T., Smee, C., Arrowsmith, C.H., Edwards, E., Bountra, C., Oppermann, U., Brennan, P.E., Yue, W.W.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	106169/ZZ14/Z

Revision History  

• Version 1.0: 2018-06-13
  Type: Initial release
  
• Version 2.0: 2018-06-27
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description