Research workbench
Ribosomal protein L11 from methanococcus jannaschii
Analyse Ribosomal protein L11 from methanococcus jannaschii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5COL
- Type
- protein
- Length
- 307 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 50S ribosomal protein L11
- UniProt
- P54030
- Ligands
- CL
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 50S ribosomal protein L11 | protein | 148 | 45% helix, 20% strand | P54030 |
| B | 50S ribosomal protein L11 | protein | 159 | 44% helix, 19% strand | P54030 |
Ligands and binding sites
- CL · Chloride ion · ion · chains A
- PGE · Triethylene glycol · additive · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains B
- CIT · Citric acid · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 466 | 0.72 | 0.82 | 44 | PGE |
| 2 | 197 | 0.66 | 0.85 | 24 | empty |
| 3 | 257 | 0.51 | 0.75 | 30 | empty |
| 4 | 79 | 0.40 | 0.78 | 10 | empty |
| 5 | 52 | 0.27 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1270 Ų buried · 12 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 P54030
- Elsewhere: RCSB PDB 5COL · PDBe 5COL · UniProt P54030
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