MolNFT v1 · #102102 · protein
Ruminococcus gnavus tryptophan decarboxylase RUMGNA_01526 (alpha-fmt)
4OBV · Pyridoxal-dependent decarboxylase domain protein: “Ruminococcus gnavus tryptophan decarboxylase RUMGNA_01526 (alpha-fmt)”. X-ray diffraction, 2 ligands (2SU, 3SO), 20 pockets (best druggability 0.83). MolNFT v1 #102102 on GenesisL1…
- PDB
- 4OBV
- Type
- protein
- Length
- 1,881 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal-dependent decarboxylase domain protein
- UniProt
- A7B1V0
- Ligands
- 2SU, 3SO
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Pyridoxal-dependent decarboxylase domain protein | protein | 469 | 48% helix, 15% strand | A7B1V0 |
| C, A | Pyridoxal-dependent decarboxylase domain protein | protein | 471 | 48% helix, 15% strand | A7B1V0 |
| B | Pyridoxal-dependent decarboxylase domain protein | protein | 470 | 47% helix, 15% strand | A7B1V0 |
Ligands and binding sites
- 2SU · alpha-(fluoromethyl)-D-tryptophan · ligand · 4 copies · chains D, B, C, A
- 3SO · {5-hydroxy-4-[(1E)-4-(1H-indol-3-yl)-3-oxobut-1-en-1-yl]-6-methylpyridin-3-yl}methyl dihydrogen phosphate · ligand · 4 copies · chains D, B, C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.83 | 0.96 | 48 | 3SO |
| 2 | 256 | 0.83 | 0.95 | 50 | 3SO |
| 3 | 233 | 0.83 | 0.95 | 46 | 3SO |
| 4 | 221 | 0.82 | 0.95 | 47 | 3SO |
| 5 | 158 | 0.80 | 0.96 | 27 | empty |
Interfaces
4 interfaces between chains.
- C–A · 6369 Ų buried · 60 hydrogen bonds · protein-protein
- D–B · 6341 Ų buried · 60 hydrogen bonds · protein-protein
- B–A · 298 Ų buried · 4 hydrogen bonds · protein-protein
- D–A · 145 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4OBV · Ruminococcus gnavus tryptophan decarboxylase RUMGNA_01526 (alpha-FMT) · the same entry in another collection · chain D against D, TM-score 1.00
- A7B1V0 · AlphaFold monomer V2.0 prediction for tryptophan decarboxylase (A7B1V0) · a predicted model of the same protein · chain B 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 A7B1V0
- Elsewhere: RCSB PDB 4OBV · PDBe 4OBV · UniProt A7B1V0
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