MolNFT v1 · #102147 · protein
Apo structure of a ubia homolog from aeropyrum pernix K1
4OD4 · 4-hydroxybenzoate octaprenyltransferase: “Apo structure of a ubia homolog from aeropyrum pernix K1”. X-ray diffraction, 20 pockets (best druggability 0.78). MolNFT v1 #102147 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4OD4
- Type
- protein
- Length
- 1,650 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxybenzoate octaprenyltransferase
- EC
- 2.5.1.-
- UniProt
- Q9YBM8
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | 4-hydroxybenzoate octaprenyltransferase (EC 2.5.1.-) | protein | 275 | 77% helix, 0% strand | Q9YBM8 |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 755 | 0.78 | 0.82 | 45 | empty |
| 2 | 717 | 0.78 | 0.82 | 43 | empty |
| 3 | 736 | 0.78 | 0.82 | 48 | empty |
| 4 | 738 | 0.78 | 0.82 | 49 | empty |
| 5 | 710 | 0.78 | 0.82 | 48 | empty |
Interfaces
5 interfaces between chains.
- B–C · 642 Ų buried · 0 hydrogen bonds · protein-protein
- E–F · 584 Ų buried · 1 hydrogen bond · protein-protein
- D–E · 484 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 474 Ų buried · 0 hydrogen bonds · protein-protein
- C–E · 208 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4OD4 · Apo structure of a UbiA homolog from Aeropyrum pernix K1 · the same entry in another collection · 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 Q9YBM8
- Elsewhere: RCSB PDB 4OD4 · PDBe 4OD4 · UniProt Q9YBM8
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