Research workbench
Crystal structure of cx-SAM bound cmob from vibrio vulnificus
Analyse Crystal structure of cx-SAM bound cmob from vibrio vulnificus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CTA
- Type
- protein
- Length
- 656 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA U34 carboxymethyltransferase
- EC
- 2.5.1.-
- UniProt
- A0A087JHK9
- Ligands
- GEK, SO4
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA U34 carboxymethyltransferase (EC 2.5.1.-) | protein | 329 | 33% helix, 26% strand | A0A087JHK9 |
| B | TRNA U34 carboxymethyltransferase (EC 2.5.1.-) | protein | 327 | 33% helix, 26% strand | A0A087JHK9 |
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
- SO4 · Sulfate 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.67 | 0.80 | 43 | GEK, SO4 |
| 2 | 382 | 0.66 | 0.80 | 41 | GEK, SO4 |
| 3 | 110 | 0.43 | 0.77 | 21 | empty |
| 4 | 111 | 0.41 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 900 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7CTA · Crystal structure of Cx-SAM bound CmoB from Vibrio vulnificus · 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
- Every structure of UniProt A0A087JHK9
- Elsewhere: RCSB PDB 7CTA · PDBe 7CTA · UniProt A0A087JHK9
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