Research workbench
Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron complexed with calcium, a closed cap conformation
Analyse Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QXG
- Type
- protein
- Length
- 445 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inorganic pyrophosphatase
- EC
- 3.6.1.1
- UniProt
- Q8A5V9
- Ligands
- CA, MG, PO4
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 222 | 49% helix, 12% strand | Q8A5V9 |
| B | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 223 | 49% helix, 12% strand | Q8A5V9 |
Ligands and binding sites
- CA · Calcium ion · metal · 7 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
- ACT · Acetate ion · additive · 5 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.76 | 0.97 | 27 | ACT, CA |
| 2 | 1025 | 0.75 | 0.78 | 60 | TLA, MG, CA |
| 3 | 151 | 0.67 | 0.88 | 36 | PO4, ACT |
| 4 | 74 | 0.33 | 0.75 | 12 | empty |
| 5 | 62 | 0.28 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 599 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3QXG · Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron complexed with… · 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 3QXG · PDBe 3QXG · UniProt Q8A5V9
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