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Inorganic pyrophosphatase (family II) from streptococcus gordonii at 1.5 a resolution
Analyse Inorganic pyrophosphatase (family II) from streptococcus gordonii at 1.5 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1K20
- Type
- protein
- Length
- 620 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
- P95765
- Ligands
- MN, SO4
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Manganese-dependent inorganic pyrophosphatase (EC 3.6.1.1) | protein | 310 | 43% helix, 20% strand | P95765 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.79 | 0.92 | 51 | SO4, GOL |
| 2 | 234 | 0.79 | 0.92 | 52 | SO4, GOL |
| 3 | 231 | 0.67 | 0.84 | 25 | empty |
| 4 | 156 | 0.58 | 0.82 | 23 | empty |
| 5 | 194 | 0.48 | 0.76 | 32 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1054 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1K20 · Inorganic Pyrophosphatase (family II) from Streptococcus gordonii at 1.5 A resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P95765 · AlphaFold monomer V2.0 prediction for probable manganese-dependent inorganic… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P95765
- Elsewhere: RCSB PDB 1K20 · PDBe 1K20 · UniProt P95765
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