2NZL

Crystal structure of human hydroxyacid oxidase 1

PDB DOI: https://doi.org/10.2210/pdb2NZL/pdb

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

Deposited: 2006-11-24 Released: 2006-12-12
Deposition Author(s): Ugochukwu, E., Kavanagh, K., Pilka, E., Berridge, G., Debreczeni, J.E., Papagrigoriou, E., Turnbull, A., Niesen, F., Gileadi, O., von Delft, F., Sundstrom, M., Arrowsmith, C.H., Weigelt, J., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.155 (Depositor), 0.150 (DCC)
R-Value Work:
0.126 (Depositor), 0.130 (DCC)
R-Value Observed:
0.126 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of human hydroxyacid oxidase 1

Ugochukwu, E., Kavanagh, K., Pilka, E., Berridge, G., Debreczeni, J.E., Papagrigoriou, E., Turnbull, A., Niesen, F., Gileadi, O., von Delft, F., Sundstrom, M., Arrowsmith, C.H., Weigelt, J., Edwards, A., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 44.07 kDa
Atom Count: 2,824
Modelled Residue Count: 339
Deposited Residue Count: 392
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxyacid oxidase 1	A	392	Homo sapiens	Mutation(s): 0 Gene Names: HAO1 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UJM8
Sequence Annotations Expand
Reference Sequence LOADING

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]
GLV Query on GLV 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]	GLYOXYLIC ACID C₂ H₂ O₃ HHLFWLYXYJOTON-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.155 (Depositor), 0.150 (DCC)
R-Value Work: 0.126 (Depositor), 0.130 (DCC)
R-Value Observed: 0.126 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.294	α = 90
b = 97.294	β = 90
c = 79.87	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
PHASER	phasing
SHELXL-97	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-12-12

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2006-12-12
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2018-01-31
Changes: Database references, Structure summary
Version 1.5: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary