Research workbench
Crystal structure of ruma, the iron-sulfur cluster containing E. COLI 23S ribosomal RNA 5-methyluridine methyltransferase
Analyse Crystal structure of ruma, the iron-sulfur cluster containing E. COLI 23S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UWV
- Type
- protein
- Length
- 417 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S rRNA (uracil-5-)-methyltransferase ruma
- EC
- 2.1.1.-
- UniProt
- P55135
- Ligands
- SF4, NI, PO4, CL
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 23S rRNA (uracil-5-)-methyltransferase ruma (EC 2.1.1.-) | protein | 417 | 26% helix, 34% strand | P55135 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A
- NI · Nickel (II) ion · metal · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 383 | 0.66 | 0.80 | 56 | SF4 |
| 2 | 111 | 0.45 | 0.79 | 21 | NI, CL |
| 3 | 77 | 0.30 | 0.73 | 16 | empty |
| 4 | 58 | 0.29 | 0.75 | 21 | empty |
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
- 1UWV · Crystal Structure of RumA, the iron-sulfur cluster containing E. coli 23S Ribosomal RNA… · the same entry in another collection · chain A against A, TM-score 1.00
- P55135 · AlphaFold monomer V2.0 prediction for 23S rRNA (URACIL(1939)-C(5))-methyltransferase rlmd… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P55135
- Elsewhere: RCSB PDB 1UWV · PDBe 1UWV · UniProt P55135
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