MolNFT v1 · #38834 · protein
Crystal structure of family II inorganic pyrophosphatase in complex with pnp
2HAW · Manganese-dependent inorganic pyrophosphatase: “Crystal structure of family II inorganic pyrophosphatase in complex with pnp”. X-ray diffraction, 5 ligands (2PN, MG, SO4), 7 pockets (best druggability 0.80). MolNFT v1 #38834 on…
- PDB
- 2HAW
- 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, MG, SO4, F, CL
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 21% 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 | 40% helix, 20% strand | P37487 |
Ligands and binding sites
- 2PN · Imidodiphosphoric acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 8 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- F · Fluoride ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 3 copies · chains B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 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 | 267 | 0.80 | 0.92 | 46 | MG, SO4, 2PN |
| 2 | 248 | 0.76 | 0.89 | 45 | MG, SO4, 2PN |
| 3 | 234 | 0.50 | 0.75 | 36 | 1PE |
| 4 | 132 | 0.47 | 0.78 | 24 | empty |
| 5 | 145 | 0.47 | 0.78 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1048 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2HAW · Crystal structure of family II Inorganic pyrophosphatase in complex with PNP · 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 2HAW · PDBe 2HAW · UniProt P37487
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