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The structure of a ribosomal protein L1 in complex with mRNA
Analyse The structure of a ribosomal protein L1 in complex with mRNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZHO
- Type
- protein + RNA
- Length
- 1,064 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MRNA; 50S ribosomal protein L1
- UniProt
- P27150
- Ligands
- K
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D, F, H | MRNA | rna | 38 | — | — |
| A, C, E, G | 50S ribosomal protein L1 | protein | 228 | 33% helix, 22% strand | P27150 |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains D, C, H, G, B, A, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 621 | 0.78 | 0.84 | 45 | empty |
| 2 | 479 | 0.76 | 0.84 | 48 | empty |
| 3 | 1093 | 0.75 | 0.79 | 62 | empty |
| 4 | 905 | 0.75 | 0.79 | 60 | empty |
| 5 | 623 | 0.72 | 0.80 | 49 | empty |
Interfaces
12 interfaces between chains.
- B–A · 1333 Ų buried · 26 hydrogen bonds · protein-nucleic
- F–E · 1255 Ų buried · 28 hydrogen bonds · protein-nucleic
- H–G · 1217 Ų buried · 24 hydrogen bonds · protein-nucleic
- D–C · 1166 Ų buried · 23 hydrogen bonds · protein-nucleic
- B–C · 774 Ų buried · 16 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 12 modified (engineered).
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 P27150
- Elsewhere: RCSB PDB 1ZHO · PDBe 1ZHO · UniProt P27150
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