MolNFT v1 · #156825 · protein
Succinyl-CoA synthase from francisella tularensis, phosphorylated, in complex with CoA
6MGG · Succinate--CoA ligase [ADP-forming] subunit alpha: “Succinyl-CoA synthase from francisella tularensis, phosphorylated, in complex with CoA”. X-ray diffraction, 2 ligands (COA, MG), 13 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 6MGG
- Type
- protein
- Length
- 1,345 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
- A0A0G2RQ73, Q5NHF3
- Ligands
- COA, MG
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinate--CoA ligase [ADP-forming] subunit alpha (EC 6.2.1.5) | protein | 293 | 35% helix, 23% strand | A0A0G2RQ73 |
| B | Succinate--CoA ligase [ADP-forming] subunit beta (EC 6.2.1.5) | protein | 387 | 38% helix, 26% strand | Q5NHF3 |
| C | Succinate--CoA ligase [ADP-forming] subunit alpha (EC 6.2.1.5) | protein | 295 | 36% helix, 23% strand | A0A0G2RQ73 |
| D | Succinate--CoA ligase [ADP-forming] subunit beta (EC 6.2.1.5) | protein | 370 | 38% helix, 26% strand | Q5NHF3 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains B, 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 878 | 0.82 | 0.84 | 106 | empty |
| 2 | 869 | 0.79 | 0.82 | 87 | EDO |
| 3 | 361 | 0.68 | 0.81 | 39 | MG |
| 4 | 257 | 0.64 | 0.82 | 42 | MG |
| 5 | 160 | 0.61 | 0.84 | 32 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2040 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1945 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 550 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 75 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6MGG · Succinyl-CoA synthase from Francisella tularensis, phosphorylated, in complex with CoA · 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 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 A0A0G2RQ73
- Every structure of UniProt Q5NHF3
- Elsewhere: RCSB PDB 6MGG · PDBe 6MGG · UniProt A0A0G2RQ73 · UniProt Q5NHF3
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