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), 0.250 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

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

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	E [auth A], G [auth B], J [auth C], L [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
BEZ (Subject of Investigation/LOI)	F [auth A], H [auth B], K [auth C], M [auth D]	BENZOIC ACID C7 H6 O2 WPYMKLBDIGXBTP-UHFFFAOYSA-N
ACT (Subject of Investigation/LOI)	I [auth B], N [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

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

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-08 
Deposition Author(s): Rachadech, W., Kato, Y., Maita, N., Fukui, K.

---

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  

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