MolNFT v1 · #156763 · protein
Succinyl-CoA synthase from campylobacter jejuni
6MEL · Succinate--CoA ligase subunit alpha: “Succinyl-CoA synthase from campylobacter jejuni”. X-ray diffraction, 1 ligand (CL), 4 pockets (best druggability 0.73). MolNFT v1 #156763 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6MEL
- Type
- protein
- Length
- 675 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinate--CoA ligase subunit alpha; Succinate--CoA ligase [ADP-forming] subunit beta
- EC
- 6.2.1.5
- UniProt
- A0A2U0Q9D2, Q5HVN3
- Ligands
- CL
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinate--CoA ligase subunit alpha | protein | 289 | 38% helix, 22% strand | A0A2U0Q9D2 |
| B | Succinate--CoA ligase [ADP-forming] subunit beta (EC 6.2.1.5) | protein | 386 | 40% helix, 26% strand | Q5HVN3 |
Ligands and binding sites
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 | 1148 | 0.73 | 0.76 | 113 | empty |
| 2 | 438 | 0.65 | 0.78 | 42 | CL, CIT |
| 3 | 52 | 0.31 | 0.76 | 10 | empty |
| 4 | 51 | 0.30 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2006 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6MEL · Succinyl-CoA synthase from Campylobacter jejuni · the same entry in another collection · chain A against A, TM-score 1.00
- Q5HVN3 · AlphaFold monomer V2.0 prediction for succinate--CoA ligase [ADP- forming] subunit beta… · a predicted model of the same protein · chain B against A, TM-score 0.96
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 A0A2U0Q9D2
- Every structure of UniProt Q5HVN3
- Elsewhere: RCSB PDB 6MEL · PDBe 6MEL · UniProt A0A2U0Q9D2 · UniProt Q5HVN3
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