Research workbench
ADP bound to ATP-grasp fold of blastocystis hominis succinyl-CoA synthetase
Analyse ADP bound to ATP-grasp fold of blastocystis hominis succinyl-CoA synthetase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NO0
- Type
- protein
- Length
- 463 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinate--CoA ligase [ADP-forming] subunit beta
- EC
- 6.2.1.5
- UniProt
- B3FHP0
- Ligands
- ADP, MG, CL
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinate--CoA ligase [ADP-forming] subunit beta (EC 6.2.1.5) | protein | 232 | 29% helix, 31% strand | B3FHP0 |
| B | Succinate--CoA ligase [ADP-forming] subunit beta (EC 6.2.1.5) | protein | 231 | 30% helix, 32% strand | B3FHP0 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · chains 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 | 108 | 0.61 | 0.87 | 20 | empty |
| 2 | 381 | 0.61 | 0.77 | 49 | ADP, MG |
| 3 | 275 | 0.57 | 0.78 | 33 | ADP, MG |
| 4 | 85 | 0.36 | 0.76 | 20 | empty |
| 5 | 51 | 0.26 | 0.73 | 10 | CL |
Interfaces
1 interface between chains.
- A–B · 1377 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6NO0 · ADP bound to ATP-grasp fold of Blastocystis hominis succinyl-CoA synthetase · the same entry in another collection · chain A against A, TM-score 1.00
- B3FHP0 · 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 0.98
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 B3FHP0
- Elsewhere: RCSB PDB 6NO0 · PDBe 6NO0 · UniProt B3FHP0
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