MolNFT v1 · #141793 · protein
Human D-amino acid oxidase complexed with 5-chlorothiophene-3- carboxylic acid
5ZJ9 · D-amino-acid oxidase: “Human D-amino acid oxidase complexed with 5-chlorothiophene-3- carboxylic acid”. X-ray diffraction, 2 ligands (FAD, 9E6), 12 pockets (best druggability 0.89). MolNFT v1 #141793 on GenesisL1: 3D structure…
- PDB
- 5ZJ9
- 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, 9E6
- Pockets
- 12 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | D-amino-acid oxidase (EC 1.4.3.3) | protein | 340 | 32% helix, 28% strand | P14920 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- 9E6 · 5-chloro thiophene-3-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
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1077 | 0.89 | 0.90 | 118 | FAD, 9E6 |
| 2 | 409 | 0.85 | 0.93 | 56 | FAD, 9E6 |
| 3 | 936 | 0.84 | 0.85 | 104 | empty |
| 4 | 599 | 0.83 | 0.88 | 69 | FAD, 9E6 |
| 5 | 885 | 0.83 | 0.85 | 111 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1716 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1698 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 737 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 733 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 117 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5ZJ9 · human D-amino acid oxidase complexed with 5-chlorothiophene-3-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 5ZJ9 · PDBe 5ZJ9 · UniProt P14920
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