6GMC

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 
    0.155 (Depositor), 0.160 (DCC) 
  • R-Value Work: 
    0.134 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 
    0.135 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FMNClick on this verticalbar to view detailsBest fitted C7CClick on this verticalbar to view details

This is version 2.1 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hydroxyacid oxidase 1368Homo sapiensMutation(s): 0 
Gene Names: HAO1GOX1HAOX1
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UJM8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
F [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
C7C
Query on C7C

Download Ideal Coordinates CCD File 
G [auth A]5-[(4-chlorophenyl)sulfanyl]-1,2,3-thiadiazole-4-carboxylate
C9 H4 Cl N2 O2 S2
NDYKFFAREALEPX-UHFFFAOYSA-M
EDO
Query on EDO

Download Ideal Coordinates CCD File 
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), 0.160 (DCC) 
  • R-Value Work:  0.134 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 0.135 (Depositor) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.348α = 90
b = 97.348β = 90
c = 80.363γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
SCALAdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FMNClick on this verticalbar to view detailsBest fitted C7CClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom106169/ZZ14/Z

Revision History  (Full details and data files)

  • 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