Research workbench
The structure of the complex between the first domain of L1 protein from thermus thermophilus and mRNA from methanococcus jannaschii
Analyse The structure of the complex between the first domain of L1 protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
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