MolNFT v1 · #141794 · protein
Human D-amino acid oxidase complexed with 5-chlorothiophene-2- carboxylic acid
5ZJA · D-amino-acid oxidase: “Human D-amino acid oxidase complexed with 5-chlorothiophene-2- carboxylic acid”. X-ray diffraction, 2 ligands (FAD, 9E9), 16 pockets (best druggability 0.88). MolNFT v1 #141794 on GenesisL1: 3D structure…
- PDB
- 5ZJA
- Type
- protein
- Length
- 1,360 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-amino-acid oxidase
- EC
- 1.4.3.3
- UniProt
- P14920
- Ligands
- FAD, 9E9
- Pockets
- 16 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | D-amino-acid oxidase (EC 1.4.3.3) | protein | 340 | 33% helix, 29% strand | P14920 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- 9E9 · 5-chloro thiophene-2-carboxylic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1039 | 0.88 | 0.89 | 120 | FAD, 9E9 |
| 2 | 1039 | 0.88 | 0.89 | 117 | FAD, 9E9 |
| 3 | 1078 | 0.84 | 0.85 | 148 | empty |
| 4 | 631 | 0.80 | 0.85 | 84 | empty |
| 5 | 123 | 0.58 | 0.84 | 24 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1713 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1710 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 713 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 683 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 71 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5ZJA · human D-amino acid oxidase complexed with 5-chlorothiophene-2-carboxylic acid · the same entry in another collection · chain A against A, TM-score 1.00
- P14920 · AlphaFold monomer V2.0 prediction for D-amino-acid oxidase (P14920) · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P14920
- Elsewhere: RCSB PDB 5ZJA · PDBe 5ZJA · UniProt P14920
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