Research workbench
Crystal structure of human 3-oxoacid CoA transferase 1
Analyse Crystal structure of human 3-oxoacid CoA transferase 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DLX
- Type
- protein
- Length
- 1,861 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
- P55809
- Pockets
- 19 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinyl-COA:3-ketoacid-coenzyme a transferase 1 (EC 2.8.3.5) | protein | 470 | 22% helix, 31% strand | P55809 |
| B | Succinyl-COA:3-ketoacid-coenzyme a transferase 1 (EC 2.8.3.5) | protein | 465 | 22% helix, 32% strand | P55809 |
| C | Succinyl-COA:3-ketoacid-coenzyme a transferase 1 (EC 2.8.3.5) | protein | 467 | 22% helix, 31% strand | P55809 |
| D | Succinyl-COA:3-ketoacid-coenzyme a transferase 1 (EC 2.8.3.5) | protein | 459 | 21% helix, 30% strand | P55809 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.85 | 0.96 | 38 | empty |
| 2 | 261 | 0.84 | 0.96 | 30 | empty |
| 3 | 981 | 0.78 | 0.80 | 95 | empty |
| 4 | 813 | 0.75 | 0.80 | 70 | empty |
| 5 | 554 | 0.72 | 0.81 | 67 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2321 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2251 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 539 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 98 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 69 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3DLX · Crystal structure of human 3-oxoacid CoA transferase 1 · the same entry in another collection · chain D against D, TM-score 1.00
- P55809 · 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 P55809
- Elsewhere: RCSB PDB 3DLX · PDBe 3DLX · UniProt P55809
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