MolNFT v1 · #141554 · protein
Crystal structure of tryptophan oxidase (C395A mutant) from chromobacterium violaceum
5ZBD · Flavin-dependent L-tryptophan oxidase vioa: “Crystal structure of tryptophan oxidase (C395A mutant) from chromobacterium violaceum”. X-ray diffraction, 2 ligands (TRP, FAD), 5 pockets (best druggability 0.84). MolNFT v1 #141554 on…
- PDB
- 5ZBD
- Type
- protein
- Length
- 825 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flavin-dependent L-tryptophan oxidase vioa
- EC
- 1.4.3.23
- UniProt
- Q9S3V1
- Ligands
- TRP, FAD
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Flavin-dependent L-tryptophan oxidase vioa (EC 1.4.3.23) | protein | 414 | 37% helix, 26% strand | Q9S3V1 |
| B | Flavin-dependent L-tryptophan oxidase vioa (EC 1.4.3.23) | protein | 411 | 38% helix, 26% strand | Q9S3V1 |
Ligands and binding sites
- TRP · Tryptophan · ligand · 2 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.84 | 0.85 | 127 | TRP, FAD |
| 2 | 1114 | 0.83 | 0.84 | 111 | TRP, FAD |
| 3 | 101 | 0.61 | 0.87 | 24 | empty |
| 4 | 96 | 0.43 | 0.78 | 16 | empty |
| 5 | 87 | 0.40 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 706 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5ZBD · Crystal structure of tryptophan oxidase (C395A mutant) from Chromobacterium violaceum · the same entry in another collection · chain B against B, TM-score 1.00
- Q9S3V1 · AlphaFold monomer V2.0 prediction for flavin-dependent L-tryptophan oxidase vioa (Q9S3V1) · 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 Q9S3V1
- Elsewhere: RCSB PDB 5ZBD · PDBe 5ZBD · UniProt Q9S3V1
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