Research workbench
Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron, GLU47ASN mutant complexed with calcium and phosphate
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
- 3QYP
- Type
- protein
- Length
- 449 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
- UNL, CA, PO4, CL
- Pockets
- 4 · best druggability 0.74
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 | 221 | 48% helix, 12% strand | Q8A5V9 |
| B | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 228 | 50% helix, 13% strand | Q8A5V9 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · chains B
- CA · Calcium ion · metal · 3 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.74 | 0.97 | 24 | PO4, GOL, UNL |
| 2 | 82 | 0.71 | 0.95 | 22 | PO4, CL |
| 3 | 97 | 0.47 | 0.80 | 23 | empty |
| 4 | 59 | 0.31 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 571 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3QYP · Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron, glu47asn mutant… · 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 3QYP · PDBe 3QYP · UniProt Q8A5V9
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