Research workbench
2.7A crystal structure of inorganic pyrophosphatase (RV3628) from mycobacterium tuberculosis at pH 7.5
Analyse 2.7A crystal structure of inorganic pyrophosphatase (RV3628) from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2UXS
- Type
- protein
- Length
- 480 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inorganic pyrophosphatase
- EC
- 3.6.1.1
- UniProt
- P65746
- Ligands
- PO4
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 160 | 21% helix, 35% strand | P65746 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 523 | 0.70 | 0.79 | 63 | empty |
| 2 | 268 | 0.57 | 0.78 | 35 | PO4 |
| 3 | 238 | 0.56 | 0.79 | 33 | PO4 |
| 4 | 209 | 0.56 | 0.79 | 30 | PO4 |
| 5 | 60 | 0.43 | 0.82 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–C · 680 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 673 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 662 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2UXS · 2.7A crystal structure of inorganic pyrophosphatase (Rv3628) from Mycobacterium… · the same entry in another collection · chain A against A, 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 P65746
- Elsewhere: RCSB PDB 2UXS · PDBe 2UXS · UniProt P65746
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