6KBP

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
R-Value Work: 0.189
R-Value Observed: 0.192

Starting Model: experimental
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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
Modelled Residue Count: 1,347
Deposited Residue Count: 1,352
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 E [auth A] SDF format, chain G [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	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 K [auth C] SDF format, chain M [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	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]

Binding Affinity Annotations
ID	Source	Binding Affinity
BEZ	BindingDB: 6KBP	IC50: 1.34e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.248
R-Value Work: 0.189
R-Value Observed: 0.192
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.493	α = 90
b = 182.783	β = 90
c = 51.039	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-07-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	18K06580
Other private	Japan	No reference number
Other private	Thailand	No reference number

Revision History (Full details and data files)

Version 1.0: 2020-07-08
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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Help and Resources

6KBP

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

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)