Research workbench
Substrate-bound structure of a ubia homolog from aeropyrum pernix K1
Analyse Substrate-bound structure of a ubia homolog from aeropyrum pernix K1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OD5
- Type
- protein
- Length
- 1,644 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
- Ligands
- GST, PHB, MG
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 70% 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 | 274 | 70% helix, 0% strand | Q9YBM8 |
Ligands and binding sites
- GST · Geranyl S-thiolodiphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- PHB · P-hydroxybenzoic acid · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.76 | 0.82 | 45 | GST, PHB, MG |
| 2 | 612 | 0.76 | 0.82 | 45 | GST, PHB, MG |
| 3 | 642 | 0.76 | 0.82 | 44 | GST, PHB, MG |
| 4 | 655 | 0.76 | 0.81 | 46 | GST, PHB, MG |
| 5 | 610 | 0.75 | 0.82 | 44 | GST, PHB, MG |
Interfaces
5 interfaces between chains.
- B–C · 693 Ų buried · 1 hydrogen bond · protein-protein
- E–F · 648 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 460 Ų buried · 0 hydrogen bonds · protein-protein
- D–E · 457 Ų buried · 0 hydrogen bonds · protein-protein
- C–E · 208 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4OD5 · Substrate-bound 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 4OD5 · PDBe 4OD5 · UniProt Q9YBM8
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