MolNFT v1 · #2558 · protein + RNA
Identification of known protein and RNA structures in a 5 a MAP of the large ribosomal subunit from haloarcula marismortui
1C04 · 23S rRNA fragment: “Identification of known protein and RNA structures in a 5 a MAP of the large ribosomal subunit from…”. X-ray diffraction, 2 pockets (best druggability 0.67). MolNFT v1 #2558 on GenesisL1: 3D structure, binding…
- PDB
- 1C04
- Type
- protein + RNA
- Length
- 575 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S rRNA fragment; Ribosomal protein L2; Ribosomal protein L6; Ribosomal protein L11…
- UniProt
- P04257, P02391, P56210, P04450
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 6 distinct chains · 18% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | 23S rRNA fragment | rna | 58 | — | — |
| F | 23S rRNA fragment | rna | 29 | — | — |
| A | Ribosomal protein L2 | protein | 135 | 2% helix, 43% strand | P04257 |
| B | Ribosomal protein L6 | protein | 164 | 21% helix, 40% strand | P02391 |
| C | Ribosomal protein L11 | protein | 67 | 58% helix, 0% strand | P56210 |
| D | Ribosomal protein L14 | protein | 122 | 8% helix, 34% strand | P04450 |
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 | 405 | 0.67 | 0.81 | 31 | empty |
| 2 | 88 | 0.29 | 0.72 | 17 | empty |
Interfaces
2 interfaces between chains.
- E–C · 1034 Ų buried · 72 hydrogen bonds · protein-nucleic
- F–B · 103 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 modified (engineered).
Compared structures
- 1C04 · Identification of known protein and RNA structures in a 5 a MAP of the large ribosomal… · the same entry in another collection · chain C against C, TM-score 1.00
- P56210 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L11 (P56210) · a predicted model of the same protein · chain C against A, TM-score 0.96
- P04257 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L2 (P04257) · a predicted model of the same protein · chain A 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 B against A, TM-score 0.95
- P04450 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L14 (P04450) · a predicted model of the same protein · chain D against A, TM-score 0.92
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 P04257
- Every structure of UniProt P02391
- Every structure of UniProt P56210
- Every structure of UniProt P04450
- Elsewhere: RCSB PDB 1C04 · PDBe 1C04 · UniProt P04257 · UniProt P02391 · UniProt P56210 · UniProt P04450
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