MolNFT v1 · #122777 · protein
The crystal structure of 50S ribosomal protein L25 from vibrio vulnificus CMCP6
5IZN: “The crystal structure of 50S ribosomal protein L25 from vibrio vulnificus CMCP6”. X-ray diffraction, 1 ligand (PO4), 8 pockets (best druggability 0.82). MolNFT v1 #122777 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.