MolNFT v1 · #52055 · protein + RNA
The structure of the complex between the first domain of L1 protein from thermus thermophilus and mRNA from methanococcus jannaschii
2VPL · 50S ribosomal protein L1: “The structure of the complex between the first domain of L1 protein from thermus thermophilus and mRNA from…”. X-ray diffraction, 1 ligand (K), 3 pockets (best druggability 0.70). MolNFT v1 #52055 on…
- PDB
- 2VPL
- Type
- protein + RNA
- Length
- 368 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 50S ribosomal protein L1; Fragment of mRNA for L1-operon containing regulator L1- binding…
- UniProt
- P27150
- Ligands
- K
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 50S ribosomal protein L1 | protein | 137 | 26% helix, 28% strand | P27150 |
| B | Fragment of mRNA for L1-operon containing regulator L1- binding site | rna | 48 | — | — |
| D | Fragment of mRNA for L1-operon containing regulator L1- binding site | rna | 46 | — | — |
Ligands and binding sites
- K · Potassium ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1156 | 0.70 | 0.75 | 52 | empty |
| 2 | 487 | 0.58 | 0.74 | 34 | empty |
| 3 | 423 | 0.56 | 0.74 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1180 Ų buried · 24 hydrogen bonds · protein-nucleic
- C–D · 1162 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–D · 452 Ų buried · 10 hydrogen bonds · nucleic-nucleic
Compared structures
- 2VPL · The structure of the complex between the first domain of L1 protein from Thermus… · the same entry in another collection · chain A against A, TM-score 1.00
- P27150 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L1 (P27150) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P27150
- Elsewhere: RCSB PDB 2VPL · PDBe 2VPL · UniProt P27150
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.