5QIH

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of HAO1 in complex with Z2697514548

PDB DOI: https://doi.org/10.2210/pdb5QIH/pdb
Deposition Group: G_1002048 (changed state) ExploreG_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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.33 Å
R-Value Free: 0.198
R-Value Work: 0.179
R-Value Observed: 0.180

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 41.45 kDa
Atom Count: 4,920
Modelled Residue Count: 344
Deposited Residue Count: 369
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJM8 (Homo sapiens) Go to UniProtKB: Q9UJM8
PHAROS: Q9UJM8 GTEx: ENSG00000101323
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain B [auth A]
GWG Query on GWG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1-methylindazole-3-carboxamide C₉ H₉ N₃ O PVROETJHCUDAFG-UHFFFAOYSA-N		Interactions Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.33 Å
R-Value Free: 0.198
R-Value Work: 0.179
R-Value Observed: 0.180
Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.46	α = 90
b = 97.46	β = 90
c = 80.52	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-07-18

Deposition Author(s):

Brandao-Neto, J.

Douangamath, A.

Arrowsmith, C.H.

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.