Research workbench
Crystal structure of the putative exported protein YPO2471 from yersinia pestis
Analyse Crystal structure of the putative exported protein YPO2471 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
- 7TEM
- Type
- protein
- Length
- 809 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative exported protein YPO2471
- UniProt
- A0A5P8YGV9
- Ligands
- GLC, FRU, CL
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative exported protein YPO2471 | protein | 404 | 52% helix, 17% strand | A0A5P8YGV9 |
| B | Putative exported protein YPO2471 | protein | 405 | 51% helix, 17% strand | A0A5P8YGV9 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
- ACY · Acetic acid · additive · chains B
- GOL · Glycerol · additive · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 706 | 0.66 | 0.75 | 66 | FRU, EDO |
| 2 | 244 | 0.49 | 0.74 | 28 | EDO, GOL |
| 3 | 199 | 0.47 | 0.75 | 31 | empty |
| 4 | 205 | 0.47 | 0.74 | 31 | ACY |
| 5 | 69 | 0.39 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 513 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 7TEM · Crystal Structure of the Putative Exported Protein YPO2471 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 A0A5P8YGV9
- Elsewhere: RCSB PDB 7TEM · PDBe 7TEM · UniProt A0A5P8YGV9
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