Research workbench
Crystal structure of basillus subtilis family II inorganic pyrophosphatase mutant, H98Q, in complex with pnp
Analyse Crystal structure of basillus subtilis family II inorganic pyrophosphatase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IW4
- Type
- protein
- Length
- 615 residues
- Chains
- 2
- 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
- 2PN, FE, MG, MN, SO4
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Manganese-dependent inorganic pyrophosphatase (EC 3.6.1.1) | protein | 307 | 41% helix, 21% strand | P37487 |
| B | Manganese-dependent inorganic pyrophosphatase (EC 3.6.1.1) | protein | 308 | 41% helix, 20% strand | P37487 |
Ligands and binding sites
- 2PN · Imidodiphosphoric acid · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- MN · Manganese (II) ion · metal · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains B
- GOL · Glycerol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.80 | 0.93 | 43 | FE, MG, MN, 2PN |
| 2 | 248 | 0.79 | 0.92 | 43 | MG, 2PN |
| 3 | 137 | 0.49 | 0.79 | 22 | empty |
| 4 | 209 | 0.48 | 0.75 | 35 | PG4 |
| 5 | 162 | 0.43 | 0.74 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 1025 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2IW4 · Crystal structure of basillus subtilis family II inorganic pyrophosphatase mutant, H98Q… · 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 A against A, TM-score 0.99
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 2IW4 · PDBe 2IW4 · UniProt P37487
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