Research workbench
Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron, a closed cap conformation
Analyse Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron, a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QU2
- Type
- protein
- Length
- 884 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inorganic pyrophosphatase
- EC
- 3.6.1.1
- UniProt
- Q8A5V9
- Ligands
- MG, CL
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 221 | 50% helix, 12% strand | Q8A5V9 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 8 copies · chains A, D, B, C
- CIT · Citric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.74 | 0.77 | 56 | empty |
| 2 | 964 | 0.73 | 0.77 | 56 | empty |
| 3 | 157 | 0.73 | 0.91 | 29 | CIT |
| 4 | 308 | 0.71 | 0.84 | 42 | GOL |
| 5 | 142 | 0.69 | 0.89 | 28 | GOL |
Interfaces
4 interfaces between chains.
- B–C · 579 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 578 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 518 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 501 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3QU2 · Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron, a closed cap… · 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 Q8A5V9
- Elsewhere: RCSB PDB 3QU2 · PDBe 3QU2 · UniProt Q8A5V9
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