MolNFT v1 · #111976 · protein
Crystal structure of inorganic pyrophosphatase from mycobacterium tuberculosis in complex with ca ions
4Z70: “Crystal structure of inorganic pyrophosphatase from mycobacterium tuberculosis in complex with ca ions”. X-ray diffraction, 1 ligand (CA), 6 pockets (best druggability 0.70). MolNFT v1 #111976 on GenesisL1: 3D structure, binding…
- PDB
- 4Z70
- Type
- protein
- Length
- 482 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
- CA
- Pockets
- 6 · 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, 38% strand | P9WI55 |
| B | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 162 | 22% helix, 36% strand | P9WI55 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 445 | 0.70 | 0.81 | 60 | empty |
| 2 | 147 | 0.51 | 0.80 | 26 | empty |
| 3 | 171 | 0.50 | 0.78 | 24 | CA |
| 4 | 146 | 0.49 | 0.79 | 26 | empty |
| 5 | 71 | 0.43 | 0.81 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 684 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 674 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 673 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4Z70 · 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 4Z70 · PDBe 4Z70 · UniProt P9WI55
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