Research workbench
Crystal structure of cx-SAM bound cmob from E. COLI in P6122
Analyse Crystal structure of cx-SAM bound cmob from E. COLI in P6122 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QNV
- Type
- protein
- Length
- 642 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (MO5U34)-methyltransferase
- EC
- 2.1.1.-
- UniProt
- A1AC32
- Ligands
- GEK, PO4
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | TRNA (MO5U34)-methyltransferase (EC 2.1.1.-) | protein | 321 | 33% helix, 25% strand | A1AC32 |
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, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.67 | 0.80 | 47 | GEK |
| 2 | 406 | 0.66 | 0.79 | 46 | GEK |
| 3 | 99 | 0.57 | 0.85 | 16 | empty |
| 4 | 112 | 0.48 | 0.80 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1000 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4QNV · Crystal structure of Cx-SAM bound CmoB from E. coli in P6122 · the same entry in another collection · chain B against B, TM-score 1.00
- A1AC32 · AlphaFold monomer V2.0 prediction for tRNA U34 carboxymethyltransferase (A1AC32) · a predicted model of the same protein · chain B 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 A1AC32
- Elsewhere: RCSB PDB 4QNV · PDBe 4QNV · UniProt A1AC32
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