Research workbench
23S ribosomal RNA G2251 2'O-methyltransferase rlmb
Analyse 23S ribosomal RNA G2251 2'O-methyltransferase rlmb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GZ0
- Type
- protein
- Length
- 1,807 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical TRNA/RRNA methyltransferase yjfh
- EC
- 2.1.1.-
- UniProt
- P39290
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hypothetical TRNA/RRNA methyltransferase yjfh (EC 2.1.1.-) | protein | 242 | 39% helix, 23% strand | P39290 |
| B, D | Hypothetical TRNA/RRNA methyltransferase yjfh (EC 2.1.1.-) | protein | 244 | 36% helix, 21% strand | P39290 |
| E, G | Hypothetical TRNA/RRNA methyltransferase yjfh (EC 2.1.1.-) | protein | 166 | 40% helix, 19% strand | P39290 |
| F | Hypothetical TRNA/RRNA methyltransferase yjfh (EC 2.1.1.-) | protein | 253 | 38% helix, 19% strand | P39290 |
| H | Hypothetical TRNA/RRNA methyltransferase yjfh (EC 2.1.1.-) | protein | 250 | 40% helix, 22% strand | P39290 |
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 764 | 0.75 | 0.80 | 73 | empty |
| 2 | 495 | 0.65 | 0.77 | 57 | empty |
| 3 | 391 | 0.62 | 0.77 | 51 | empty |
| 4 | 413 | 0.61 | 0.77 | 46 | empty |
| 5 | 277 | 0.60 | 0.79 | 34 | empty |
Interfaces
11 interfaces between chains.
- A–F · 1279 Ų buried · 25 hydrogen bonds · protein-protein
- C–H · 1271 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1251 Ų buried · 25 hydrogen bonds · protein-protein
- B–G · 1239 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 557 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 58 modified (engineered).
Compared structures
- 1GZ0 · 23S ribosomal RNA G2251 2'O-methyltransferase rlmb · the same entry in another collection · chain A against A, TM-score 1.00
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 P39290
- Elsewhere: RCSB PDB 1GZ0 · PDBe 1GZ0 · UniProt P39290
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