6KBP | pdb_00006kbp

Crystal structure of human D-amino acid oxidase mutant (P219L) complexed with benzoate

PDB DOI: https://doi.org/10.2210/pdb6KBP/pdb

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

Deposited: 2019-06-26 Released: 2020-07-08
Deposition Author(s): Rachadech, W., Kato, Y., Maita, N., Fukui, K.
Funding Organization(s): Japan Society for the Promotion of Science, Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.248 (Depositor), 0.227 (DCC)
R-Value Work:
0.189 (Depositor)
R-Value Observed:
0.192 (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 D-amino acid oxidase mutant (P219L) complexed with benzoate

Rachadech, W., Kato, Y., Maita, N., Fukui, K.

To be published.

Macromolecule Content

Total Structure Weight: 157.81 kDa
Atom Count: 11,479
Modeled Residue Count: 1,347
Deposited Residue Count: 1,352
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-amino-acid oxidase	A, B, C, D	338	Homo sapiens	Mutation(s): 1 Gene Names: DAO, DAMOX EC: 1.4.3.3
UniProt & NIH Common Fund Data Resources
Find proteins for P14920 (Homo sapiens) Explore P14920 Go to UniProtKB: P14920
PHAROS: P14920 GTEx: ENSG00000110887
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14920
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], J [auth C], L [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D]
BEZ (Subject of Investigation/LOI) Query on BEZ Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain M [auth D] SDF format, chain K [auth C] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C]	F [auth A], H [auth B], K [auth C], M [auth D]	BENZOIC ACID C₇ H₆ O₂ WPYMKLBDIGXBTP-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D]
ACT (Subject of Investigation/LOI) Query on ACT Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain N [auth D] MOL2 format, chain I [auth B] MOL2 format, chain N [auth D] mmCIF format, chain I [auth B] mmCIF format, chain N [auth D]	I [auth B], N [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain I [auth B] Focus chain N [auth D] Interactions & Density Focus chain I [auth B] Focus chain N [auth D]