Research workbench
Crystal structure of exopolyphosphatase from yersinia pestis
Analyse Crystal structure of exopolyphosphatase from yersinia pestis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RF0
- Type
- protein
- Length
- 397 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exopolyphosphatase
- EC
- 3.6.1.11
- UniProt
- Q7CJK2
- Ligands
- NO3
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exopolyphosphatase (EC 3.6.1.11) | protein | 199 | 60% helix, 9% strand | Q7CJK2 |
| B | Exopolyphosphatase (EC 3.6.1.11) | protein | 198 | 62% helix, 9% strand | Q7CJK2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.74 | 0.77 | 64 | FMT |
| 2 | 142 | 0.52 | 0.80 | 20 | empty |
| 3 | 60 | 0.33 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 274 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 3RF0 · Crystal Structure of Exopolyphosphatase from Yersinia pestis · 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 Q7CJK2
- Elsewhere: RCSB PDB 3RF0 · PDBe 3RF0 · UniProt Q7CJK2
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