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Crystal structure of inorganic pyrophosphatase from mycobacterium tuberculosis in complex with inorganic pyrophosphate
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
- 4Z74
- 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, CA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F, G, E, H, I, K, L | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 160 | 21% helix, 38% strand | P9WI55 |
| J | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 161 | 22% helix, 35% strand | P9WI55 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 12 copies · chains A, B, C, D, F, G, E, H, I, J, K, L
- CA · Calcium ion · metal · 44 copies · chains A, B, C, D, F, G, E, H, I, J, K, L
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 | 726 | 0.81 | 0.84 | 64 | empty |
| 2 | 882 | 0.80 | 0.83 | 72 | empty |
| 3 | 978 | 0.79 | 0.81 | 77 | empty |
| 4 | 682 | 0.79 | 0.83 | 54 | empty |
| 5 | 667 | 0.78 | 0.83 | 65 | empty |
Interfaces
26 interfaces between chains.
- G–I · 700 Ų buried · 13 hydrogen bonds · protein-protein
- J–L · 690 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 689 Ų buried · 11 hydrogen bonds · protein-protein
- J–K · 689 Ų buried · 12 hydrogen bonds · protein-protein
- K–L · 683 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4Z74 · 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 4Z74 · PDBe 4Z74 · UniProt P9WI55
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