Research workbench
Crystal structure of inorganic pyrophosphatase from mycobacterium tuberculosis in complex with mg ions
Analyse Crystal structure of inorganic pyrophosphatase from mycobacterium tuberculosis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z71
- Type
- protein
- Length
- 483 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inorganic pyrophosphatase
- EC
- 3.6.1.1
- UniProt
- P9WI55
- Ligands
- MG
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 160 | 22% helix, 37% strand | P9WI55 |
| B | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 163 | 21% helix, 36% strand | P9WI55 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 513 | 0.70 | 0.79 | 67 | empty |
| 2 | 206 | 0.54 | 0.78 | 29 | MG |
| 3 | 203 | 0.51 | 0.77 | 28 | MG |
| 4 | 183 | 0.50 | 0.77 | 24 | empty |
| 5 | 58 | 0.44 | 0.83 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 682 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 667 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 657 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4Z71 · Crystal structure of inorganic pyrophosphatase from Mycobacterium tuberculosis in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WI55 · AlphaFold monomer V2.0 prediction for inorganic pyrophosphatase (P9WI55) · 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 P9WI55
- Elsewhere: RCSB PDB 4Z71 · PDBe 4Z71 · UniProt P9WI55
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