Research workbench
C28S mutant of succinyl-COA:3-ketoacid CoA transferase from pig heart
Analyse C28S mutant of succinyl-COA:3-ketoacid CoA transferase from pig heart in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NRB
- Type
- protein
- Length
- 1,873 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinyl-COA:3-ketoacid-coenzyme a transferase 1
- EC
- 2.8.3.5
- UniProt
- Q29551
- Ligands
- CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Succinyl-COA:3-ketoacid-coenzyme a transferase 1 (EC 2.8.3.5) | protein | 467 | 22% helix, 32% strand | Q29551 |
| B | Succinyl-COA:3-ketoacid-coenzyme a transferase 1 (EC 2.8.3.5) | protein | 470 | 22% helix, 33% strand | Q29551 |
| D | Succinyl-COA:3-ketoacid-coenzyme a transferase 1 (EC 2.8.3.5) | protein | 469 | 22% helix, 32% strand | Q29551 |
Ligands and binding sites
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 644 | 0.85 | 0.90 | 82 | empty |
| 2 | 219 | 0.84 | 0.97 | 30 | empty |
| 3 | 214 | 0.84 | 0.97 | 29 | empty |
| 4 | 401 | 0.81 | 0.89 | 51 | empty |
| 5 | 499 | 0.70 | 0.80 | 71 | CL |
Interfaces
3 interfaces between chains.
- C–D · 2417 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 2391 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 1271 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2NRB · C28S Mutant of Succinyl-CoA:3-Ketoacid CoA Transferase from Pig Heart · the same entry in another collection · chain A against A, TM-score 1.00
- Q29551 · AlphaFold monomer V2.0 prediction for succinyl-COA:3-ketoacid coenzyme a transferase 1… · a predicted model of the same protein · chain A 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 Q29551
- Elsewhere: RCSB PDB 2NRB · PDBe 2NRB · UniProt Q29551
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