MolNFT v1 · #32128 · protein + RNA
Crystal structure of E. COLI 5-methyluridine methyltransferase ruma in complex with ribosomal RNA substrate and S-adenosylhomocysteine.
2BH2 · 23S rRNA (uracil-5-)-methyltransferase ruma: “Crystal structure of E. COLI 5-methyluridine methyltransferase ruma in complex with ribosomal RNA substrate…”. X-ray diffraction, 2 ligands (SAH, SF4), 12 pockets (best druggability…
- PDB
- 2BH2
- Type
- protein + RNA
- Length
- 894 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S rRNA (uracil-5-)-methyltransferase ruma; 23S ribosomal RNA 1932-1968
- EC
- 2.1.1.-
- UniProt
- P55135
- Ligands
- SAH, SF4
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 23S rRNA (uracil-5-)-methyltransferase ruma (EC 2.1.1.-) | protein | 418 | 26% helix, 34% strand | P55135 |
| B | 23S rRNA (uracil-5-)-methyltransferase ruma (EC 2.1.1.-) | protein | 416 | 26% helix, 34% strand | P55135 |
| C, D | 23S ribosomal RNA 1932-1968 | rna | 30 | — | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, C, B, D
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, C, B, D
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 | 723 | 0.80 | 0.84 | 90 | SAH |
| 2 | 299 | 0.78 | 0.90 | 50 | SAH |
| 3 | 998 | 0.72 | 0.76 | 59 | empty |
| 4 | 781 | 0.68 | 0.76 | 53 | empty |
| 5 | 259 | 0.61 | 0.80 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2285 Ų buried · 69 hydrogen bonds · protein-nucleic
- B–D · 2169 Ų buried · 67 hydrogen bonds · protein-nucleic
- A–B · 936 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 2BH2 · Crystal Structure of E. coli 5-methyluridine methyltransferase RumA in complex with… · the same entry in another collection · chain B against B, 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 0.99
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 2BH2 · PDBe 2BH2 · UniProt P55135
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