MolNFT v1 · #92637 · protein
Crystal structure of wild-type cmoa from E.COLI
4GEK · TRNA (CMO5U34)-methyltransferase: “Crystal structure of wild-type cmoa from E.COLI”. X-ray diffraction, 2 ligands (GEK, SO4), 7 pockets (best druggability 0.69). MolNFT v1 #92637 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4GEK
- Type
- protein
- Length
- 461 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (CMO5U34)-methyltransferase
- EC
- 2.1.1.-
- Ligands
- GEK, SO4
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (CMO5U34)-methyltransferase (EC 2.1.1.-) | protein | 230 | 47% helix, 23% strand | — |
| G | TRNA (CMO5U34)-methyltransferase (EC 2.1.1.-) | protein | 231 | 46% helix, 23% strand | — |
Ligands and binding sites
- GEK · (2S)-4-[{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(carboxylatomethyl)sulfonio] -2-ammoniobutanoate · ligand · 2 copies · chains A, G
- SO4 · Sulfate ion · ion · 3 copies · chains A, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 247 | 0.69 | 0.85 | 43 | GEK |
| 2 | 263 | 0.66 | 0.83 | 49 | SO4, GEK |
| 3 | 97 | 0.43 | 0.78 | 26 | empty |
| 4 | 105 | 0.39 | 0.75 | 24 | empty |
| 5 | 66 | 0.35 | 0.77 | 17 | SO4 |
Interfaces
1 interface between chains.
- A–G · 1422 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4GEK · Crystal Structure of wild-type CmoA from E.coli · 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
- Elsewhere: RCSB PDB 4GEK · PDBe 4GEK
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