7R4P | pdb_00007r4p

Structure of human hydroxyacid oxidase 1 bound with 6-amino-1-benzyl-5-(methylamino)pyrimidine-2,4(1H,3H)-dione

PDB DOI: https://doi.org/10.2210/pdb7R4P/pdb

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

Deposited: 2022-02-09 Released: 2022-05-04
Deposition Author(s): Mackinnon, S., Bezerra, G.A., Krojer, T., Bradley, A.R., Talon, R., Brandeo-Neto, J., Douangamath, A., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Oppermann, U., Brennan, P.E., Yue, W.W.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.37 Å
R-Value Free:
0.196 (Depositor), 0.196 (DCC)
R-Value Work:
0.180 (Depositor), 0.179 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure of human hydroxyacid oxidase 1 bound with 5-bromo-N-methyl-1H-indazole-3-carboxamide

Mackinnon, S., Bezerra, G.A., Krojer, T., Bradley, A.R., Talon, R., Brandeo-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: 40.86 kDa
Atom Count: 2,941
Modeled Residue Count: 337
Deposited Residue Count: 362
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxyacid oxidase 1	A	362	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UJM8
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] Interactions & Density Focus chain B [auth A]
I2Z (Subject of Investigation/LOI) Query on I2Z 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]	6-amino-1-benzyl-5-(methylamino)pyrimidine-2,4(1H,3H)-dione C₁₂ H₁₆ N₄ O₂ ROGMXQYZAWKCLY-ZJUUUORDSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.37 Å
R-Value Free: 0.196 (Depositor), 0.196 (DCC)
R-Value Work: 0.180 (Depositor), 0.179 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.13	α = 90
b = 97.13	β = 90
c = 80.84	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-05-04

Deposition Author(s):

Brandeo-Neto, J.

Douangamath, A.

Arrowsmith, C.H.

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	092809/Z/10/Z

Revision History (Full details and data files)

Version 1.0: 2022-05-04
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.