Research workbench
The crystal structure of 50S ribosomal protein L25 from vibrio vulnificus CMCP6
Analyse The crystal structure of 50S ribosomal protein L25 from vibrio vulnificus CMCP6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IZN
- Type
- protein
- Length
- 742 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 50S ribosomal protein L25
- UniProt
- Q8D8W6
- Ligands
- PO4
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 50S ribosomal protein L25 | protein | 94 | 16% helix, 39% strand | Q8D8W6 |
| C, E, G | 50S ribosomal protein L25 | protein | 93 | 17% helix, 46% strand | Q8D8W6 |
| D, H | 50S ribosomal protein L25 | protein | 92 | 17% helix, 48% strand | Q8D8W6 |
| F | 50S ribosomal protein L25 | protein | 91 | 16% helix, 38% strand | Q8D8W6 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 8 copies · chains A, C, B, D, E, G, H, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1160 | 0.82 | 0.83 | 94 | PO4 |
| 2 | 1176 | 0.81 | 0.82 | 96 | PO4 |
| 3 | 51 | 0.36 | 0.79 | 14 | empty |
| 4 | 86 | 0.32 | 0.74 | 15 | empty |
| 5 | 78 | 0.31 | 0.74 | 15 | empty |
Interfaces
11 interfaces between chains.
- A–B · 2094 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 2077 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 641 Ų buried · 10 hydrogen bonds · protein-protein
- E–H · 588 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 562 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 5IZN · The crystal structure of 50S ribosomal protein L25 from Vibrio vulnificus CMCP6 · the same entry in another collection · chain H against H, TM-score 1.00
- Q8D8W6 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L25 (Q8D8W6) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 Q8D8W6
- Elsewhere: RCSB PDB 5IZN · PDBe 5IZN · UniProt Q8D8W6
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