5WWV

Crystal structure of porcine kidney D-amino acid oxidase mutant (I230A/R283G)

PDB DOI: https://doi.org/10.2210/pdb5WWV/pdb

Classification: OXIDOREDUCTASE
Organism(s): Sus scrofa
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2017-01-05 Released: 2018-01-17
Deposition Author(s): Motojima, F., Yasukawa, K., Ohno, A., Asano, Y.
Funding Organization(s): JST

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.242
R-Value Work: 0.145
R-Value Observed: 0.150

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

Tailoring D-amino acid oxidase from the pid kidney to R-stereoselective amine oxidase and its use in the deracemization of 4-chlorobenzhydrylamine

Yasukawa, K., Motojima, F., Ohno, A., Asano, Y.

To be published.

Macromolecule Content

Total Structure Weight: 324.32 kDa
Atom Count: 22,427
Modelled Residue Count: 2,707
Deposited Residue Count: 2,776
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, E A, B, C, D, E, F, G, H	347	Sus scrofa	Mutation(s): 2 Gene Names: DAO EC: 1.4.3.3
UniProt
Find proteins for P00371 (Sus scrofa) Explore P00371 Go to UniProtKB: P00371
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00371
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain HA [auth F] SDF format, chain I [auth A] SDF format, chain NA [auth G] SDF format, chain P [auth B] SDF format, chain RA [auth H] SDF format, chain S [auth C] SDF format, chain W [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain HA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain NA [auth G] MOL2 format, chain P [auth B] MOL2 format, chain RA [auth H] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain HA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain NA [auth G] mmCIF format, chain P [auth B] mmCIF format, chain RA [auth H] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D]	BA [auth E] HA [auth F] I [auth A] NA [auth G] P [auth B] BA [auth E], HA [auth F], I [auth A], NA [auth G], P [auth B], RA [auth H], S [auth C], W [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain BA [auth E] Focus chain HA [auth F] Focus chain I [auth A] Focus chain NA [auth G] Focus chain P [auth B] Focus chain RA [auth H] Focus chain S [auth C] Focus chain W [auth D] Interactions & Density Focus chain BA [auth E] Focus chain HA [auth F] Focus chain I [auth A] Focus chain NA [auth G] Focus chain P [auth B] Focus chain RA [auth H] Focus chain S [auth C] Focus chain W [auth D]
7V3 Query on 7V3 Download Ideal Coordinates CCD File SDF format, chain IA [auth F] SDF format, chain J [auth A] SDF format, chain OA [auth G] SDF format, chain T [auth C] SDF format, chain X [auth D] MOL2 format, chain IA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain OA [auth G] MOL2 format, chain T [auth C] MOL2 format, chain X [auth D] mmCIF format, chain IA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain OA [auth G] mmCIF format, chain T [auth C] mmCIF format, chain X [auth D]	IA [auth F], J [auth A], OA [auth G], T [auth C], X [auth D]	(S)-(4-chlorophenyl)-phenyl-methanamine C₁₃ H₁₂ Cl N XAFODXGEQUOEKN-ZDUSSCGKSA-N		Interactions Focus chain IA [auth F] Focus chain J [auth A] Focus chain OA [auth G] Focus chain T [auth C] Focus chain X [auth D] Interactions & Density Focus chain IA [auth F] Focus chain J [auth A] Focus chain OA [auth G] Focus chain T [auth C] Focus chain X [auth D]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain EA [auth E] SDF format, chain GA [auth E] SDF format, chain JA [auth F] SDF format, chain K [auth A] SDF format, chain KA [auth F] SDF format, chain L [auth A] SDF format, chain LA [auth F] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain PA [auth G] SDF format, chain Q [auth B] SDF format, chain QA [auth G] SDF format, chain R [auth B] SDF format, chain SA [auth H] SDF format, chain TA [auth H] SDF format, chain U [auth C] SDF format, chain UA [auth H] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain GA [auth E] MOL2 format, chain JA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain PA [auth G] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth G] MOL2 format, chain R [auth B] MOL2 format, chain SA [auth H] MOL2 format, chain TA [auth H] MOL2 format, chain U [auth C] MOL2 format, chain UA [auth H] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain CA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain GA [auth E] mmCIF format, chain JA [auth F] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth F] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain PA [auth G] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth G] mmCIF format, chain R [auth B] mmCIF format, chain SA [auth H] mmCIF format, chain TA [auth H] mmCIF format, chain U [auth C] mmCIF format, chain UA [auth H] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	CA [auth E] DA [auth E] EA [auth E] GA [auth E] JA [auth F] CA [auth E], DA [auth E], EA [auth E], GA [auth E], JA [auth F], K [auth A], KA [auth F], L [auth A], LA [auth F], M [auth A], N [auth A], PA [auth G], Q [auth B], QA [auth G], R [auth B], SA [auth H], TA [auth H], U [auth C], UA [auth H], Y [auth D], Z [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain GA [auth E] Focus chain JA [auth F] Focus chain K [auth A] Focus chain KA [auth F] Focus chain L [auth A] Focus chain LA [auth F] Focus chain M [auth A] Focus chain N [auth A] Focus chain PA [auth G] Focus chain Q [auth B] Focus chain QA [auth G] Focus chain R [auth B] Focus chain SA [auth H] Focus chain TA [auth H] Focus chain U [auth C] Focus chain UA [auth H] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain GA [auth E] Focus chain JA [auth F] Focus chain K [auth A] Focus chain KA [auth F] Focus chain L [auth A] Focus chain LA [auth F] Focus chain M [auth A] Focus chain N [auth A] Focus chain PA [auth G] Focus chain Q [auth B] Focus chain QA [auth G] Focus chain R [auth B] Focus chain SA [auth H] Focus chain TA [auth H] Focus chain U [auth C] Focus chain UA [auth H] Focus chain Y [auth D] Focus chain Z [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain FA [auth E] SDF format, chain MA [auth F] SDF format, chain O [auth A] SDF format, chain V [auth C] SDF format, chain VA [auth H] MOL2 format, chain AA [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain MA [auth F] MOL2 format, chain O [auth A] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth H] mmCIF format, chain AA [auth D] mmCIF format, chain FA [auth E] mmCIF format, chain MA [auth F] mmCIF format, chain O [auth A] mmCIF format, chain V [auth C] mmCIF format, chain VA [auth H]	AA [auth D] FA [auth E] MA [auth F] O [auth A] V [auth C] AA [auth D], FA [auth E], MA [auth F], O [auth A], V [auth C], VA [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain FA [auth E] Focus chain MA [auth F] Focus chain O [auth A] Focus chain V [auth C] Focus chain VA [auth H] Interactions & Density Focus chain AA [auth D] Focus chain FA [auth E] Focus chain MA [auth F] Focus chain O [auth A] Focus chain V [auth C] Focus chain VA [auth H]