MolNFT v1 · #125966 · protein
Crystal structure of SCP2 thiolase from leishmania mexicana. complex of the C123A mutant with acetyl-CoA.
5LOT · 3-ketoacyl-CoA thiolase-like protein: “Crystal structure of SCP2 thiolase from leishmania mexicana. complex of the C123A mutant with acetyl-CoA.”. X-ray diffraction, 1 ligand (ACO), 16 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 5LOT
- Type
- protein
- Length
- 1,720 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-ketoacyl-CoA thiolase-like protein
- EC
- 2.3.1.16
- UniProt
- E9AW84
- Ligands
- ACO
- Pockets
- 16 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 3-ketoacyl-CoA thiolase-like protein (EC 2.3.1.16) | protein | 430 | 40% helix, 16% strand | E9AW84 |
Ligands and binding sites
- ACO · Acetyl coenzyme *A · ligand · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.79 | 0.84 | 98 | empty |
| 2 | 417 | 0.74 | 0.84 | 48 | empty |
| 3 | 378 | 0.74 | 0.84 | 47 | ACO |
| 4 | 475 | 0.73 | 0.82 | 63 | ACO |
| 5 | 393 | 0.72 | 0.83 | 49 | ACO |
Interfaces
4 interfaces between chains.
- A–B · 2493 Ų buried · 55 hydrogen bonds · protein-protein
- C–D · 2476 Ų buried · 57 hydrogen bonds · protein-protein
- B–C · 439 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 206 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5LOT · Crystal structure of SCP2 thiolase from Leishmania mexicana. Complex of the C123A mutant… · the same entry in another collection · 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 E9AW84
- Elsewhere: RCSB PDB 5LOT · PDBe 5LOT · UniProt E9AW84
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