5QIB | pdb_00005qib

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of HAO1 in complex with FMOPL000388a

• PDB DOI: https://doi.org/10.2210/pdb5QIB/pdb
• Deposition Group: G_1002048 (changed state) | Explore  G_1002048  

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


• Deposited: 2018-05-22 Released: 2018-07-18 
• Deposition Author(s): MacKinnon, S., Bezerra, G.A., Krojer, T., Bradley, A.R., Talon, R., Brandao-Neto, J., Douangamath, A., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Oppermann, U., Brennan, P.E., Yue, W.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands)

MacKinnon, S., Bezerra, G.A., Krojer, T., Bradley, A.R., Talon, R., Brandao-Neto, J., Douangamath, A., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Oppermann, U., Brennan, P.E., Yue, W.W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 41.49 kDa 
• Atom Count: 4,298 
• Modeled Residue Count: 344 
• Deposited Residue Count: 369 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxyacid oxidase 1	A	369	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FNR	B [auth A]	1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL C17 H23 N4 O9 P YTNIXZGTHTVJBW-SCRDCRAPSA-N
GX7	C [auth A]	5-(cyclohexylamino)pyrimidine-2,4(1H,3H)-dione C10 H15 N3 O2 WHMIGQGVTIZZPV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.996	α = 90
b = 97.996	β = 90
c = 81.741	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-07-18 
Deposition Author(s): MacKinnon, S., Bezerra, G.A., Krojer, T., Bradley, A.R., Talon, R., Brandao-Neto, J., Douangamath, A., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Oppermann, U., Brennan, P.E., Yue, W.W.

Revision History  

• Version 1.0: 2018-07-18
  Type: Initial release
  
• Version 1.1: 2018-08-15
  Changes: Data collection, Database references
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references
• Version 1.3: 2026-02-18
  Changes: Refinement description, Structure summary