MolNFT v1 · #11952 · protein
Inorganic pyrophosphatase (family II) from bacillus subtilis
1K23 · Manganese-dependent inorganic pyrophosphatase: “Inorganic pyrophosphatase (family II) from bacillus subtilis”. X-ray diffraction, 1 ligand (MN), 15 pockets (best druggability 0.76). MolNFT v1 #11952 on GenesisL1: 3D structure…
- PDB
- 1K23
- Type
- protein
- Length
- 1,153 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Manganese-dependent inorganic pyrophosphatase
- EC
- 3.6.1.1
- UniProt
- P37487
- Ligands
- MN
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Manganese-dependent inorganic pyrophosphatase (EC 3.6.1.1) | protein | 307 | 40% helix, 20% strand | P37487 |
| C | Manganese-dependent inorganic pyrophosphatase (EC 3.6.1.1) | protein | 308 | 40% helix, 20% strand | P37487 |
| D | Manganese-dependent inorganic pyrophosphatase (EC 3.6.1.1) | protein | 231 | 39% helix, 15% strand | P37487 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.76 | 0.78 | 71 | empty |
| 2 | 247 | 0.49 | 0.74 | 21 | empty |
| 3 | 223 | 0.48 | 0.74 | 26 | empty |
| 4 | 218 | 0.47 | 0.74 | 34 | empty |
| 5 | 160 | 0.44 | 0.75 | 26 | empty |
Interfaces
4 interfaces between chains.
- A–B · 837 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 829 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 336 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 83 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 1K23 · Inorganic Pyrophosphatase (Family II) from Bacillus subtilis · the same entry in another collection · chain A against A, TM-score 1.00
- P37487 · AlphaFold monomer V2.0 prediction for manganese-dependent inorganic pyrophosphatase… · a predicted model of the same protein · chain D against A, TM-score 0.89
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 P37487
- Elsewhere: RCSB PDB 1K23 · PDBe 1K23 · UniProt P37487
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