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ADP bound to K46BE&K114BD mutant ATP-grasp fold of blastocystis hominis succinyl-CoA synthetase
Analyse ADP bound to K46BE&K114BD mutant ATP-grasp fold of blastocystis hominis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NO5
- Type
- protein
- Length
- 927 residues
- Chains
- 4
- 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, NH4
- Pockets
- 10 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinate--CoA ligase [ADP-forming] subunit beta (EC 6.2.1.5) | protein | 239 | 30% helix, 30% strand | B3FHP0 |
| B | Succinate--CoA ligase [ADP-forming] subunit beta (EC 6.2.1.5) | protein | 234 | 29% helix, 31% strand | B3FHP0 |
| C | Succinate--CoA ligase [ADP-forming] subunit beta (EC 6.2.1.5) | protein | 221 | 28% helix, 33% strand | B3FHP0 |
| D | Succinate--CoA ligase [ADP-forming] subunit beta (EC 6.2.1.5) | protein | 233 | 30% helix, 32% strand | B3FHP0 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- NH4 · Ammonium ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.65 | 0.91 | 18 | empty |
| 2 | 66 | 0.64 | 0.93 | 16 | empty |
| 3 | 353 | 0.60 | 0.77 | 42 | ADP, MG |
| 4 | 310 | 0.60 | 0.78 | 41 | ADP, MG |
| 5 | 278 | 0.59 | 0.79 | 35 | ADP, MG |
Interfaces
3 interfaces between chains.
- C–D · 1369 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1346 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 54 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6NO5 · ADP bound to K46bE&K114bD mutant ATP-grasp fold of Blastocystis hominis succinyl-CoA… · the same entry in another collection · chain D against D, 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 C 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 6NO5 · PDBe 6NO5 · UniProt B3FHP0
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