Research workbench
Crystal structure of L-tryptophan oxidase vioa from chromobacterium violaceum in complex with 5-methyl-L-tryptophan
Analyse Crystal structure of L-tryptophan oxidase vioa from chromobacterium violaceum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FW8
- Type
- protein
- Length
- 834 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
- FAD, D0Q, MG
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Flavin-dependent L-tryptophan oxidase vioa (EC 1.4.3.23) | protein | 417 | 35% helix, 26% strand | Q9S3V1 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains B, A
- D0Q · 5-methyl-L-tryptophan · ligand · 2 copies · chains B, A
- MG · Magnesium ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 994 | 0.86 | 0.86 | 108 | FAD, D0Q, MG |
| 2 | 857 | 0.85 | 0.87 | 94 | FAD, D0Q, MG |
| 3 | 138 | 0.46 | 0.78 | 21 | empty |
| 4 | 90 | 0.46 | 0.80 | 18 | empty |
| 5 | 97 | 0.45 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- B–A · 688 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6FW8 · Crystal structure of L-tryptophan oxidase VioA from Chromobacterium violaceum in complex… · 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 B 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 6FW8 · PDBe 6FW8 · UniProt Q9S3V1
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