MolNFT v1 · #40024 · protein
Crystal structure of 3-octaprenyl-4-hydroxybenzoate decarboxylase (ubid) from escherichia COLI, northeast structural genomics target ER459.
2IDB · 3-octaprenyl-4-hydroxybenzoate carboxy-lyase: “Crystal structure of 3-octaprenyl-4-hydroxybenzoate decarboxylase (ubid) from escherichia COLI, northeast…”. X-ray diffraction, 16 pockets (best druggability 0.82). MolNFT v1 #40024 on…
- PDB
- 2IDB
- Type
- protein
- Length
- 1,385 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
- EC
- 4.1.1.-
- UniProt
- P0AAB4
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (EC 4.1.1.-) | protein | 474 | 30% helix, 27% strand | P0AAB4 |
| B | 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (EC 4.1.1.-) | protein | 455 | 28% helix, 27% strand | P0AAB4 |
| C | 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (EC 4.1.1.-) | protein | 456 | 28% helix, 24% strand | P0AAB4 |
Ligands and binding sites
- 1PE · Pentaethylene glycol · additive · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.82 | 0.83 | 64 | EDO |
| 2 | 99 | 0.81 | 0.99 | 17 | empty |
| 3 | 1155 | 0.80 | 0.81 | 71 | 1PE |
| 4 | 1101 | 0.77 | 0.79 | 94 | empty |
| 5 | 90 | 0.46 | 0.81 | 24 | empty |
Interfaces
2 interfaces between chains.
- A–B · 4081 Ų buried · 60 hydrogen bonds · protein-protein
- B–C · 1099 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 2IDB · Crystal Structure of 3-octaprenyl-4-hydroxybenzoate decarboxylase (UbiD) from Escherichia… · the same entry in another collection · chain A against A, TM-score 1.00
- P0AAB4 · AlphaFold monomer V2.0 prediction for 3-octaprenyl-4-hydroxybenzoate carboxy-lyase… · a predicted model of the same protein · chain C against A, TM-score 0.96
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 P0AAB4
- Elsewhere: RCSB PDB 2IDB · PDBe 2IDB · UniProt P0AAB4
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