6H00 | pdb_00006h00

Crystal structure of human pyridoxine 5-phophate oxidase, R116Q variant

PDB DOI: https://doi.org/10.2210/pdb6H00/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2018-07-05 Released: 2018-08-08
Deposition Author(s): Mackinnon, S., Wilson, M.P., Shrestha, L., Bezerra, G.A., Newman, J., Fox, N., Sorrell, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Clayton, P.T., Mills, P.B., Yue, W.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free:
0.203 (Depositor), 0.210 (DCC)
R-Value Work:
0.169 (Depositor), 0.181 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of human pyridoxine 5-phophate oxidase, R116Q variant

Mackinnon, S., Wilson, M.P., Shrestha, L., Bezerra, G.A., Newman, J., Fox, N., Sorrell, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Clayton, P.T., Mills, P.B., Yue, W.W.

To be published.

Macromolecule Content

Total Structure Weight: 30.99 kDa
Atom Count: 1,762
Modeled Residue Count: 204
Deposited Residue Count: 261
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxine-5'-phosphate oxidase	A	261	Homo sapiens	Mutation(s): 1 Gene Names: PNPO EC: 1.4.3.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NVS9 (Homo sapiens) Explore Q9NVS9 Go to UniProtKB: Q9NVS9
PHAROS: Q9NVS9 GTEx: ENSG00000108439
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NVS9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]