Research workbench
Crystal structure of SCP2 thiolase from leishmania mexicana: the C123A mutant.
Analyse Crystal structure of SCP2 thiolase from leishmania mexicana: the C123A mutant. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZBK
- Type
- protein
- Length
- 860 residues
- Chains
- 2
- 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
- CL
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-ketoacyl-CoA thiolase-like protein (EC 2.3.1.16) | protein | 430 | 39% helix, 17% strand | E9AW84 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 7 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 414 | 0.75 | 0.84 | 48 | DMS, CL |
| 2 | 388 | 0.72 | 0.83 | 46 | DMS, CL |
| 3 | 314 | 0.65 | 0.81 | 62 | DMS |
| 4 | 89 | 0.42 | 0.78 | 15 | empty |
| 5 | 67 | 0.38 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2470 Ų buried · 56 hydrogen bonds · protein-protein
Compared structures
- 3ZBK · Crystal structure of SCP2 thiolase from Leishmania mexicana: 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 3ZBK · PDBe 3ZBK · UniProt E9AW84
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