Research workbench
Inorganic pyrophosphatase from mycobacterium tuberculosis in complex with inhibitor 6 and inorganic pyrophosphate
Analyse Inorganic pyrophosphatase from mycobacterium tuberculosis in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KDF
- Type
- protein
- Length
- 161 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inorganic pyrophosphatase
- EC
- 3.6.1.1
- UniProt
- P9WI55
- Ligands
- 6RU, POP, CA
- Pockets
- 1 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 161 | 22% helix, 35% strand | P9WI55 |
Ligands and binding sites
- 6RU · ~{N}2,~{N}2,~{N}4,~{N}4-tetramethyl-6-(1-phenylpyrrol-2-yl)-1,3,5-triazine-2,4-diamine · ligand · chains A
- POP · Pyrophosphate 2- · ligand · chains A
- CA · Calcium ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.52 | 0.79 | 21 | CA, POP |
Compared structures
- 5KDF · Inorganic pyrophosphatase from Mycobacterium tuberculosis in complex with inhibitor 6 and… · 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 5KDF · PDBe 5KDF · UniProt P9WI55
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