Research workbench
Crystal structure of L-tryptophan oxidase vioa from chromobacterium violaceum
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
- 6ESD
- Type
- protein
- Length
- 827 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, CL
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Flavin-dependent L-tryptophan oxidase vioa (EC 1.4.3.23) | protein | 415 | 35% helix, 26% strand | Q9S3V1 |
| A | Flavin-dependent L-tryptophan oxidase vioa (EC 1.4.3.23) | protein | 412 | 35% helix, 26% strand | Q9S3V1 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains B, A
- CL · Chloride ion · ion · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.85 | 0.86 | 97 | FAD, CL |
| 2 | 1018 | 0.85 | 0.86 | 114 | FAD, CL |
| 3 | 247 | 0.52 | 0.76 | 29 | empty |
| 4 | 273 | 0.52 | 0.75 | 29 | empty |
| 5 | 133 | 0.49 | 0.79 | 29 | empty |
Interfaces
1 interface between chains.
- B–A · 717 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6ESD · Crystal structure of L-tryptophan oxidase VioA 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 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 6ESD · PDBe 6ESD · UniProt Q9S3V1
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