Download MendeleyCrystal structure of DAAO variant
Nakano, S., Yasukawa, K., Kawahara, N., Ishitsubo, E., Tokiwa, H., Asano, Y.To be published.
4YJG
Crystal structure of DAAO(Y228L/R283G) variant (R-3-amino 1-phenylbutane binding form)
- PDB DOI: https://doi.org/10.2210/pdb4YJG/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Sus scrofa
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2015-03-03 Released: 2016-04-06
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.237
- R-Value Work: 0.190
- R-Value Observed: 0.192
Starting Model: experimental
View more details
This is version 1.2 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| D-amino-acid oxidase | 341 | 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 AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| D-amino-acid oxidase | 340 | 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 AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| FAD Query on FAD | D [auth A], H [auth B] | FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N |  | ||
| 4DD Query on 4DD | C [auth A], G [auth B] | (2R)-4-phenylbutan-2-amine C10 H15 N WECUIGDEWBNQJJ-SECBINFHSA-N |  | ||
| SO4 Query on SO4 | E [auth A], F [auth A], I [auth B], J [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.237
- R-Value Work: 0.190
- R-Value Observed: 0.192
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 68.59 | α = 90 |
| b = 92.114 | β = 90 |
| c = 110.274 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2016-04-06 Deposition Author(s): Nakano, S., Yasukawa, K., Kawahara, N., Ishitsubo, E., Tokiwa, H., Asano, Y.
Revision History (Full details and data files)
- Version 1.0: 2016-04-06
Type: Initial release - Version 1.1: 2017-09-27
Changes: Data collection, Database references, Derived calculations - Version 1.2: 2023-11-08
Changes: Data collection, Database references, Refinement description
