Research workbench
Pyrophosphatase with ppi from acinetobacter baumannii
Analyse Pyrophosphatase with ppi from acinetobacter baumannii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K27
- Type
- protein
- Length
- 1,384 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inorganic pyrophosphatase
- EC
- 3.6.1.1
- UniProt
- N9S5K0
- Ligands
- DPO, MG
- Pockets
- 19 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 173 | 19% helix, 35% strand | N9S5K0 |
Ligands and binding sites
- DPO · Diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 24 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 576 | 0.72 | 0.80 | 77 | DPO, MG |
| 2 | 406 | 0.64 | 0.78 | 44 | empty |
| 3 | 221 | 0.57 | 0.79 | 33 | DPO, MG |
| 4 | 254 | 0.56 | 0.78 | 36 | DPO, MG |
| 5 | 177 | 0.55 | 0.80 | 35 | DPO, MG |
Interfaces
10 interfaces between chains.
- D–H · 670 Ų buried · 6 hydrogen bonds · protein-protein
- C–G · 664 Ų buried · 6 hydrogen bonds · protein-protein
- A–F · 661 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 445 Ų buried · 3 hydrogen bonds · protein-protein
- D–G · 430 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6K27 · Pyrophosphatase with PPi from Acinetobacter baumannii · 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 N9S5K0
- Elsewhere: RCSB PDB 6K27 · PDBe 6K27 · UniProt N9S5K0
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