MolNFT v1 · #141553 · protein
Crystal structure of se-met tryptophan oxidase (C395A mutant) from chromobacterium violaceum
5ZBC · Flavin-dependent L-tryptophan oxidase vioa: “Crystal structure of se-met tryptophan oxidase (C395A mutant) from chromobacterium violaceum”. X-ray diffraction, 1 ligand (FAD), 6 pockets (best druggability 0.85). MolNFT v1 #141553 on…
- PDB
- 5ZBC
- Type
- protein
- Length
- 818 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
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Flavin-dependent L-tryptophan oxidase vioa (EC 1.4.3.23) | protein | 413 | 37% helix, 25% strand | Q9S3V1 |
| B | Flavin-dependent L-tryptophan oxidase vioa (EC 1.4.3.23) | protein | 405 | 38% helix, 25% strand | Q9S3V1 |
Ligands and binding sites
- 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
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 934 | 0.85 | 0.86 | 103 | FAD |
| 2 | 1082 | 0.84 | 0.85 | 124 | FAD |
| 3 | 228 | 0.49 | 0.75 | 25 | empty |
| 4 | 88 | 0.43 | 0.79 | 13 | empty |
| 5 | 75 | 0.43 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 639 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 5ZBC · Crystal structure of Se-Met tryptophan oxidase (C395A mutant) from Chromobacterium… · the same entry in another collection · chain A against A, 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 5ZBC · PDBe 5ZBC · UniProt Q9S3V1
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