MolNFT v1 · #17503 · protein
Crystal structure of indolepyruvate decarboxylase from enterobacter cloacae
1OVM · Indole-3-pyruvate decarboxylase: “Crystal structure of indolepyruvate decarboxylase from enterobacter cloacae”. X-ray diffraction, 2 ligands (TPP, MG), 20 pockets (best druggability 0.84). MolNFT v1 #17503 on GenesisL1: 3D…
- PDB
- 1OVM
- Type
- protein
- Length
- 2,140 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Indole-3-pyruvate decarboxylase
- EC
- 4.1.1.74
- UniProt
- P23234
- Ligands
- TPP, MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Indole-3-pyruvate decarboxylase (EC 4.1.1.74) | protein | 535 | 42% helix, 17% strand | P23234 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
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 | 271 | 0.84 | 0.95 | 59 | MG, TPP |
| 2 | 370 | 0.83 | 0.92 | 77 | MG, TPP |
| 3 | 222 | 0.83 | 0.96 | 41 | MG, TPP |
| 4 | 213 | 0.82 | 0.96 | 43 | MG, TPP |
| 5 | 615 | 0.77 | 0.83 | 75 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3585 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 3555 Ų buried · 44 hydrogen bonds · protein-protein
- A–C · 923 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 921 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 182 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1OVM · Crystal structure of Indolepyruvate decarboxylase from Enterobacter cloacae · the same entry in another collection · chain D against D, TM-score 1.00
- P23234 · AlphaFold monomer V2.0 prediction for indole-3-pyruvate decarboxylase (P23234) · 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 P23234
- Elsewhere: RCSB PDB 1OVM · PDBe 1OVM · UniProt P23234
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