MolNFT v1 · #37146 · protein
Crystal structure of yebu, a M5C RNA methyltransferase from E.COLI
2FRX · Hypothetical protein yebu: “Crystal structure of yebu, a M5C RNA methyltransferase from E.COLI”. X-ray diffraction, 20 pockets (best druggability 0.74). MolNFT v1 #37146 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2FRX
- Type
- protein
- Length
- 1,818 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein yebu
- UniProt
- P76273
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Hypothetical protein yebu | protein | 455 | 32% helix, 23% strand | P76273 |
| B, C | Hypothetical protein yebu | protein | 454 | 32% helix, 23% strand | P76273 |
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.74 | 0.77 | 66 | empty |
| 2 | 579 | 0.66 | 0.77 | 67 | empty |
| 3 | 276 | 0.58 | 0.78 | 40 | empty |
| 4 | 309 | 0.55 | 0.75 | 37 | empty |
| 5 | 305 | 0.54 | 0.75 | 41 | empty |
Interfaces
4 interfaces between chains.
- A–B · 536 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 243 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 64 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 12 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 2FRX · Crystal structure of YebU, a m5C RNA methyltransferase from E.coli · the same entry in another collection · chain A against A, TM-score 1.00
- P76273 · AlphaFold monomer V2.0 prediction for ribosomal RNA small subunit methyltransferase F… · 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 P76273
- Elsewhere: RCSB PDB 2FRX · PDBe 2FRX · UniProt P76273
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