2NZL | pdb_00002nzl

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), 0.149 (DCC)
R-Value Work:
0.126 (Depositor), 0.130 (DCC)
R-Value Observed:
0.126 (Depositor)

Starting Models: experimental
View more details

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
Modeled Residue Count: 339
Deposited Residue Count: 392
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 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% 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]
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), 0.149 (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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

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