MolNFT v1 · #154651 · protein
Pyrophosphatase mutant K149R from acinetobacter baumannii
6KI8 · Inorganic pyrophosphatase: “Pyrophosphatase mutant K149R from acinetobacter baumannii”. X-ray diffraction, 2 ligands (DPO, MG), 7 pockets (best druggability 0.77). MolNFT v1 #154651 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6KI8
- Type
- protein
- Length
- 519 residues
- Chains
- 3
- 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
- 7 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 173 | 19% helix, 33% strand | N9S5K0 |
Ligands and binding sites
- DPO · Diphosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 9 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 794 | 0.77 | 0.80 | 59 | empty |
| 2 | 378 | 0.60 | 0.77 | 48 | DPO, MG |
| 3 | 333 | 0.57 | 0.76 | 42 | DPO, MG |
| 4 | 286 | 0.57 | 0.77 | 41 | DPO, MG |
| 5 | 63 | 0.35 | 0.77 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 584 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 583 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 574 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6KI8 · Pyrophosphatase mutant K149R 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 6KI8 · PDBe 6KI8 · UniProt N9S5K0
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