Research workbench
Structure of inorganic pyrophosphatase from escherichia COLI in complex with sulfate
Analyse Structure of inorganic pyrophosphatase from escherichia COLI in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UM4
- Type
- protein
- Length
- 525 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inorganic pyrophosphatase
- EC
- 3.6.1.1
- UniProt
- P0A7A9
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 175 | 18% helix, 33% strand | P0A7A9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.85 | 0.94 | 33 | empty |
| 2 | 308 | 0.62 | 0.79 | 39 | SO4 |
| 3 | 399 | 0.62 | 0.77 | 35 | empty |
| 4 | 230 | 0.58 | 0.79 | 32 | SO4 |
| 5 | 203 | 0.57 | 0.80 | 33 | SO4 |
Interfaces
3 interfaces between chains.
- A–B · 704 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 701 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 694 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4UM4 · Structure of inorganic pyrophosphatase from escherichia COLI in complex with sulfate · the same entry in another collection · chain A against A, TM-score 1.00
- P0A7A9 · AlphaFold monomer V2.0 prediction for inorganic pyrophosphatase (P0A7A9) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P0A7A9
- Elsewhere: RCSB PDB 4UM4 · PDBe 4UM4 · UniProt P0A7A9
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