Research workbench
Bdellovibrio bacteriovorus pgi in P1211 spacegroup
Analyse Bdellovibrio bacteriovorus pgi in P1211 spacegroup in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7O0A
- Type
- protein
- Length
- 3,236 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose-6-phosphate isomerase
- EC
- 5.3.1.9
- UniProt
- Q6MPU9
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G, H | Glucose-6-phosphate isomerase (EC 5.3.1.9) | protein | 404 | 55% helix, 15% strand | Q6MPU9 |
| B, D, F, E | Glucose-6-phosphate isomerase (EC 5.3.1.9) | protein | 405 | 54% helix, 15% strand | Q6MPU9 |
Ligands and binding sites
- ACT · Acetate ion · additive · 4 copies · chains D, F, A, E
- EDO · 1,2-ethanediol · additive · 2 copies · chains C, H, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.85 | 0.86 | 98 | ACT |
| 2 | 1060 | 0.85 | 0.86 | 94 | EDO |
| 3 | 1057 | 0.84 | 0.85 | 91 | ACT |
| 4 | 727 | 0.80 | 0.84 | 62 | empty |
| 5 | 301 | 0.78 | 0.90 | 47 | empty |
Interfaces
13 interfaces between chains.
- D–F · 5291 Ų buried · 88 hydrogen bonds · protein-protein
- B–G · 5245 Ų buried · 88 hydrogen bonds · protein-protein
- A–E · 5181 Ų buried · 86 hydrogen bonds · protein-protein
- C–H · 5164 Ų buried · 89 hydrogen bonds · protein-protein
- C–D · 507 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7O0A · Bdellovibrio bacteriovorus PGI in P1211 spacegroup · 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 Q6MPU9
- Elsewhere: RCSB PDB 7O0A · PDBe 7O0A · UniProt Q6MPU9
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