Research workbench
The structure of the L-tryptophan oxidase vioa from chromobacterium violaceum
Analyse The structure of the 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
- 5G3T
- Type
- protein
- Length
- 1,652 residues
- Chains
- 4
- 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, MG, CL
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-tryptophan oxidase vioa (EC 1.4.3.23) | protein | 413 | 38% helix, 26% strand | Q9S3V1 |
| C | L-tryptophan oxidase vioa (EC 1.4.3.23) | protein | 414 | 37% helix, 26% strand | Q9S3V1 |
| D | L-tryptophan oxidase vioa (EC 1.4.3.23) | protein | 412 | 37% helix, 26% strand | Q9S3V1 |
Ligands and binding sites
- FDA · Dihydroflavine-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 6 copies · chains A, B, D
- CL · Chloride ion · ion · 11 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains B, C, D
- GOL · Glycerol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 867 | 0.85 | 0.87 | 100 | FDA, MG, CL |
| 2 | 931 | 0.85 | 0.87 | 102 | FDA, MG, CL, TRS |
| 3 | 883 | 0.85 | 0.87 | 107 | FDA, CL, TRS |
| 4 | 1027 | 0.85 | 0.86 | 107 | FDA, CL, TRS |
| 5 | 391 | 0.61 | 0.77 | 36 | empty |
Interfaces
4 interfaces between chains.
- A–B · 659 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 555 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 262 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 151 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 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 1.00
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 5G3T · PDBe 5G3T · UniProt Q9S3V1
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