Research workbench
Succinyl-CoA:3-ketoacid CoA transferase from pig heart covalently bound to CoA
Analyse Succinyl-CoA:3-ketoacid CoA transferase from pig heart covalently bound to CoA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OXO
- Type
- protein
- Length
- 3,710 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Sus scrofa
- Molecule
- Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial
- EC
- 2.8.3.5
- UniProt
- Q29551
- Ligands
- COA, CL
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · resolution 2.3 · 8 distinct chains · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial (EC 2.8.3.5) | protein | 469 | 22% helix, 33% strand | Q29551 |
| B | Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial (EC 2.8.3.5) | protein | 466 | 21% helix, 33% strand | Q29551 |
| C | Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial (EC 2.8.3.5) | protein | 466 | 22% helix, 33% strand | Q29551 |
| D | Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial (EC 2.8.3.5) | protein | 467 | 22% helix, 33% strand | Q29551 |
| E | Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial (EC 2.8.3.5) | protein | 462 | 21% helix, 34% strand | Q29551 |
| F | Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial (EC 2.8.3.5) | protein | 463 | 20% helix, 33% strand | Q29551 |
| G | Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial (EC 2.8.3.5) | protein | 459 | 20% helix, 34% strand | Q29551 |
| H | Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial (EC 2.8.3.5) | protein | 458 | 20% helix, 34% strand | Q29551 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 4 copies · chains E, F, G, H
- CL · Chloride ion · ion · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 264 | 0.84 | 0.96 | 42 | empty |
| 2 | 261 | 0.84 | 0.96 | 40 | empty |
| 3 | 262 | 0.84 | 0.96 | 34 | empty |
| 4 | 245 | 0.84 | 0.97 | 29 | empty |
| 5 | 1051 | 0.80 | 0.82 | 108 | empty |
Interfaces
12 interfaces between chains.
- A–B · 2476 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 2474 Ų buried · 45 hydrogen bonds · protein-protein
- G–H · 2438 Ų buried · 43 hydrogen bonds · protein-protein
- E–F · 2405 Ų buried · 38 hydrogen bonds · protein-protein
- D–H · 570 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 3OXO · Succinyl-COA:3-ketoacid CoA transferase from pig heart covalently bound to CoA · the same entry in another collection · chain H against H, 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 B 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 3OXO · PDBe 3OXO · UniProt Q29551
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