Research workbench
Seven ribosomal proteins fitted to a cryo-electron microscopic MAP of the large 50S subunit at 7.5 ångströms resolution
Analyse Seven ribosomal proteins fitted to a cryo-electron microscopic MAP of the large… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 487D
- Type
- protein
- Length
- 1,021 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (50S L1 ribosomal protein); Protein (50S L2 ribosomal protein); Protein (50S L6…
- UniProt
- P27150, P04257, P02391, P02417, P29395, P04450, P02426
- Ligands
- NH2
- Pockets
- 2 · best druggability 0.71
Structure
electron microscopy · 7 distinct chains · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Protein (50S L1 ribosomal protein) | protein | 224 | 32% helix, 22% strand | P27150 |
| I | Protein (50S L2 ribosomal protein) | protein | 135 | 2% helix, 43% strand | P04257 |
| J | Protein (50S L6 ribosomal protein) | protein | 164 | 21% helix, 40% strand | P02391 |
| K | Protein (50S L9 ribosomal protein) | protein | 149 | 40% helix, 33% strand | P02417 |
| L | Protein (50S L11 ribosomal protein) | protein | 133 | 38% helix, 16% strand | P29395 |
| M | Protein (50S L14 ribosomal protein) | protein | 122 | 8% helix, 34% strand | P04450 |
| N | Protein (50S L25 ribosomal protein) | protein | 94 | 22% helix, 45% strand | P02426 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.71 | 0.79 | 53 | empty |
| 2 | 113 | 0.35 | 0.73 | 29 | empty |
Interfaces
1 interface between chains.
- I–K · 37 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified, 1 covalent (engineered, additive adduct).
Compared structures
- 487D · Seven ribosomal proteins fitted to a cryo-electron microscopic MAP of the large 50S… · the same entry in another collection · chain L against L, TM-score 1.00
- 1OLN · Model for thiostrepton antibiotic binding to L11 substrate from 50S ribosomal RNA · a predicted model of the same protein · chain L against A, TM-score 0.98
- 1OLN · Model for thiostrepton antibiotic binding to L11 substrate from 50S ribosomal RNA · a predicted model of the same protein · chain L against A, TM-score 0.98
- P04257 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L2 (P04257) · a predicted model of the same protein · chain I against A, TM-score 0.96
- P02391 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L6 (P02391) · a predicted model of the same protein · chain J against A, TM-score 0.95
- P29395 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L11 (P29395) · a predicted model of the same protein · chain L against A, TM-score 0.93
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
- Every structure of UniProt P04257
- Every structure of UniProt P02391
- Every structure of UniProt P02417
- Every structure of UniProt P29395
- Every structure of UniProt P04450
- Every structure of UniProt P02426
- Elsewhere: RCSB PDB 487D · PDBe 487D · UniProt P27150 · UniProt P04257 · UniProt P02391 · UniProt P02417 · UniProt P29395 · UniProt P04450 · UniProt P02426
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.