Research workbench
Yaxa from yersinia enterocolitica
Analyse Yaxa from yersinia enterocolitica in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EK7
- Type
- protein
- Length
- 364 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yaxa
- UniProt
- A0A0T9S5R5
- Pockets
- 4 · best druggability 0.37
Structure
x-ray diffraction · 1 distinct chain · 82% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yaxa | protein | 364 | 82% helix, 2% strand | A0A0T9S5R5 |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 9 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.37 | 0.78 | 12 | MPD |
| 2 | 59 | 0.31 | 0.75 | 12 | MPD |
| 3 | 66 | 0.31 | 0.74 | 14 | empty |
| 4 | 58 | 0.30 | 0.74 | 13 | MPD |
Compared structures
- 6EK7 · YaxA from Yersinia enterocolitica · 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 A0A0T9S5R5
- Elsewhere: RCSB PDB 6EK7 · PDBe 6EK7 · UniProt A0A0T9S5R5
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