MolNFT v1 · #175523 · protein
Crystal structure of sah bound cmob from vibrio vulnificus
7CT9 · TRNA U34 carboxymethyltransferase: “Crystal structure of sah bound cmob from vibrio vulnificus”. X-ray diffraction, 2 ligands (SAH, PO4), 4 pockets (best druggability 0.68). MolNFT v1 #175523 on GenesisL1: 3D structure, binding…
- PDB
- 7CT9
- 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
- SAH, PO4
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | TRNA U34 carboxymethyltransferase (EC 2.5.1.-) | protein | 328 | 32% helix, 26% strand | A0A087JHK9 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- MLI · Malonate ion · additive · 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 | 405 | 0.68 | 0.81 | 44 | SAH, MLI, PO4 |
| 2 | 402 | 0.65 | 0.79 | 41 | SAH, MLI, PO4 |
| 3 | 125 | 0.41 | 0.75 | 18 | empty |
| 4 | 106 | 0.40 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 705 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7CT9 · Crystal structure of SAH 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 7CT9 · PDBe 7CT9 · UniProt A0A087JHK9
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