Research workbench
Crystal structure of the escherichia COLI ycei protein, structural genomics
Analyse Crystal structure of the escherichia COLI ycei protein, structural genomics in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y0G
- Type
- protein
- Length
- 676 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein ycei
- UniProt
- P0A8X2
- Ligands
- 8PP
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Protein ycei | protein | 169 | 12% helix, 57% strand | P0A8X2 |
Ligands and binding sites
- 8PP · 2-[(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaenyl]phenol · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 435 | 0.85 | 0.91 | 54 | 8PP |
| 2 | 461 | 0.84 | 0.90 | 56 | 8PP |
| 3 | 463 | 0.83 | 0.90 | 59 | 8PP |
| 4 | 462 | 0.82 | 0.89 | 59 | 8PP |
| 5 | 300 | 0.70 | 0.84 | 56 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1544 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 1542 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 323 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
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 P0A8X2
- Elsewhere: RCSB PDB 1Y0G · PDBe 1Y0G · UniProt P0A8X2
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