MolNFT v1 · #168343 · protein
Tartryl-CoA bound to human GTP-specific succinyl-CoA synthetase
6WCV · Succinate--CoA ligase [ADP/GDP-forming] subunit alpha…: “Tartryl-CoA bound to human GTP-specific succinyl-CoA synthetase”. X-ray diffraction, 1 ligand (TUY), 5 pockets (best druggability 0.78). MolNFT v1 #168343 on GenesisL1: 3D…
- PDB
- 6WCV
- Type
- protein
- Length
- 699 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial; Succinate--CoA…
- EC
- 6.2.1.4, 6.2.1.5
- UniProt
- P53597, Q96I99
- Ligands
- TUY
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial (EC 6.2.1.4, 6.2.1.5) | protein | 306 | 38% helix, 21% strand | P53597 |
| B | Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial (EC 6.2.1.4) | protein | 393 | 37% helix, 25% strand | Q96I99 |
Ligands and binding sites
- TUY · (3S,5S,9R,20R,21R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9,20, 21-pentahydroxy-8,8-dimethyl-10,14,19-trioxo-2,4,6-trioxa-18-thia-11,15-diaza-3,5-diphosphadocosan-22-oic acid 3,5-dioxide (non-preferred name) · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.78 | 0.80 | 91 | empty |
| 2 | 564 | 0.76 | 0.83 | 66 | TUY |
| 3 | 151 | 0.58 | 0.83 | 27 | empty |
| 4 | 67 | 0.32 | 0.75 | 17 | empty |
| 5 | 59 | 0.30 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2143 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 6WCV · Tartryl-CoA bound to human GTP-specific succinyl-CoA synthetase · the same entry in another collection · chain A against A, TM-score 1.00
- P53597 · AlphaFold monomer V2.0 prediction for succinate--CoA ligase [ADP/GDP- forming] subunit… · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q96I99 · AlphaFold monomer V2.0 prediction for succinate--CoA ligase [GDP- forming] subunit beta… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P53597
- Every structure of UniProt Q96I99
- Elsewhere: RCSB PDB 6WCV · PDBe 6WCV · UniProt P53597 · UniProt Q96I99
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