Research workbench
Putative solute-binding protein from yersinia pestis.
Analyse Putative solute-binding protein 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
- 3RY3
- Type
- protein
- Length
- 979 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative solute-binding protein
- UniProt
- Q7CJS8
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative solute-binding protein | protein | 489 | 26% helix, 25% strand | Q7CJS8 |
| B | Putative solute-binding protein | protein | 490 | 25% helix, 24% strand | Q7CJS8 |
Ligands and binding sites
- ACT · Acetate ion · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 742 | 0.78 | 0.82 | 83 | empty |
| 2 | 572 | 0.76 | 0.83 | 66 | empty |
| 3 | 406 | 0.61 | 0.77 | 48 | empty |
| 4 | 219 | 0.60 | 0.81 | 26 | empty |
| 5 | 245 | 0.55 | 0.78 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 978 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3RY3 · Putative solute-binding protein 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 Q7CJS8
- Elsewhere: RCSB PDB 3RY3 · PDBe 3RY3 · UniProt Q7CJS8
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