MolNFT v1 · #119688 · protein
The structure of the L-tryptophan oxidase vioa from chromobacterium violaceum in complex with its inhibitor 2-(1H-indol-3-YLMETHYL)PROP- 2- enoic acid
5G3U: “The structure of the L-tryptophan oxidase vioa from chromobacterium violaceum in complex with its inhibitor…”. X-ray diffraction, 2 ligands (FDA, ITW), 8 pockets (best druggability 0.82). MolNFT v1 #119688 on GenesisL1: 3D…
- PDB
- 5G3U
- Type
- protein
- Length
- 824 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-tryptophan oxidase vioa
- EC
- 1.4.3.23
- UniProt
- Q9S3V1
- Ligands
- FDA, ITW
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-tryptophan oxidase vioa (EC 1.4.3.23) | protein | 412 | 38% helix, 27% strand | Q9S3V1 |
Ligands and binding sites
- FDA · Dihydroflavine-adenine dinucleotide · ligand · 2 copies · chains A, B
- ITW · 2-[(1H-indol-3-yl)methyl]prop-2-enoic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 936 | 0.82 | 0.83 | 99 | FDA, ITW |
| 2 | 1114 | 0.81 | 0.82 | 113 | FDA, ITW |
| 3 | 94 | 0.64 | 0.89 | 25 | empty |
| 4 | 85 | 0.61 | 0.88 | 22 | empty |
| 5 | 335 | 0.56 | 0.76 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 749 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 5G3U · The structure of the L-tryptophan oxidase VioA from Chromobacterium violaceum in complex… · 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 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 5G3U · PDBe 5G3U · UniProt Q9S3V1
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