MolNFT v1 · #160274 · protein
Succinyl-CoA synthase from francisella tularensis
6PFN · Succinate--CoA ligase [ADP-forming] subunit alpha: “Succinyl-CoA synthase from francisella tularensis”. X-ray diffraction, 1 ligand (COA), 13 pockets (best druggability 0.78). MolNFT v1 #160274 on GenesisL1: 3D structure, binding…
- PDB
- 6PFN
- Type
- protein
- Length
- 1,250 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinate--CoA ligase [ADP-forming] subunit alpha; Succinate--CoA ligase [ADP-forming]…
- EC
- 6.2.1.5
- UniProt
- A0A454XSD0, Q5NHF3
- Ligands
- COA
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinate--CoA ligase [ADP-forming] subunit alpha (EC 6.2.1.5) | protein | 295 | 36% helix, 23% strand | A0A454XSD0 |
| B | Succinate--CoA ligase [ADP-forming] subunit beta (EC 6.2.1.5) | protein | 326 | 35% helix, 28% strand | Q5NHF3 |
| C | Succinate--CoA ligase [ADP-forming] subunit alpha (EC 6.2.1.5) | protein | 293 | 34% helix, 23% strand | A0A454XSD0 |
| D | Succinate--CoA ligase [ADP-forming] subunit beta (EC 6.2.1.5) | protein | 336 | 37% helix, 27% strand | Q5NHF3 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 2 copies · chains A, B, C
- ACT · Acetate ion · additive · chains D
- EDO · 1,2-ethanediol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 838 | 0.78 | 0.81 | 70 | empty |
| 2 | 826 | 0.78 | 0.81 | 81 | empty |
| 3 | 272 | 0.66 | 0.83 | 38 | COA |
| 4 | 184 | 0.65 | 0.85 | 33 | empty |
| 5 | 644 | 0.63 | 0.73 | 45 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2023 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1854 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 234 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 54 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6PFN · Succinyl-CoA synthase from Francisella tularensis · the same entry in another collection · chain A against A, TM-score 1.00
- Q5NHF3 · AlphaFold monomer V2.0 prediction for succinate--CoA ligase [ADP- forming] subunit beta… · a predicted model of the same protein · chain D 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 A0A454XSD0
- Every structure of UniProt Q5NHF3
- Elsewhere: RCSB PDB 6PFN · PDBe 6PFN · UniProt A0A454XSD0 · UniProt Q5NHF3
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