MolNFT v1 · #111979 · protein
Crystal structure of inorganic pyrophosphatase from mycobacterium tuberculosis in complex with a phosphate ion and an inorganic pyrophosphate
4Z73: “Crystal structure of inorganic pyrophosphatase from mycobacterium tuberculosis in complex with a phosphate…”. X-ray diffraction, 3 ligands (POP, MN, PO4), 20 pockets (best druggability 0.79). MolNFT v1 #111979 on GenesisL1: 3D…
- PDB
- 4Z73
- Type
- protein
- Length
- 1,921 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inorganic pyrophosphatase
- EC
- 3.6.1.1
- UniProt
- P9WI55
- Ligands
- POP, MN, PO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, F, G, E, H, I, J, K, L | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 160 | 21% helix, 37% strand | P9WI55 |
| D | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 161 | 20% helix, 36% strand | P9WI55 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 3 copies · chains B, K, L
- MN · Manganese (II) ion · metal · 27 copies · chains A, B, C, D, F, G, E, H, I, J, K, L
- PO4 · Phosphate ion · ion · 9 copies · chains A, C, D, F, G, E, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 926 | 0.79 | 0.81 | 78 | empty |
| 2 | 603 | 0.79 | 0.84 | 55 | empty |
| 3 | 646 | 0.79 | 0.83 | 50 | empty |
| 4 | 629 | 0.78 | 0.83 | 49 | empty |
| 5 | 581 | 0.78 | 0.84 | 49 | empty |
Interfaces
26 interfaces between chains.
- F–E · 710 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 698 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 695 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 693 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 692 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4Z73 · Crystal structure of inorganic pyrophosphatase from Mycobacterium tuberculosis in complex… · the same entry in another collection · chain L against L, TM-score 1.00
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 4Z73 · PDBe 4Z73 · UniProt P9WI55
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