Research workbench
Crystal structure of ycjy from E. COLI
Analyse Crystal structure of ycjy from E. COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XB6
- Type
- protein
- Length
- 3,671 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein ycjy
- UniProt
- P76049
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, K, L | Uncharacterized protein ycjy | protein | 306 | 41% helix, 19% strand | P76049 |
| J | Uncharacterized protein ycjy | protein | 305 | 41% helix, 19% strand | P76049 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 894 | 0.84 | 0.86 | 116 | empty |
| 2 | 901 | 0.84 | 0.85 | 112 | empty |
| 3 | 952 | 0.80 | 0.82 | 114 | empty |
| 4 | 689 | 0.77 | 0.82 | 77 | empty |
| 5 | 94 | 0.76 | 0.97 | 25 | empty |
Interfaces
18 interfaces between chains.
- E–F · 1977 Ų buried · 24 hydrogen bonds · protein-protein
- I–J · 1976 Ų buried · 26 hydrogen bonds · protein-protein
- K–L · 1974 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1973 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1960 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 5XB6 · Crystal structure of YcjY from E. Coli · the same entry in another collection · chain L against L, 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 P76049
- Elsewhere: RCSB PDB 5XB6 · PDBe 5XB6 · UniProt P76049
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