MolNFT v1 · #84139 · protein
Crystal structure of wild-type SCP2 thiolase from leishmania mexicana at 1.85 a
3ZBG · 3-ketoacyl-CoA thiolase-like protein: “Crystal structure of wild-type SCP2 thiolase from leishmania mexicana at 1.85 a”. X-ray diffraction, 8 pockets (best druggability 0.70). MolNFT v1 #84139 on GenesisL1: 3D structure, binding…
- PDB
- 3ZBG
- Type
- protein
- Length
- 862 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
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-ketoacyl-CoA thiolase-like protein (EC 2.3.1.16) | protein | 431 | 39% helix, 16% strand | E9AW84 |
Ligands and binding sites
- DMS · Dimethyl sulfoxide · additive · 14 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.70 | 0.83 | 42 | DMS, MPD |
| 2 | 372 | 0.70 | 0.82 | 42 | DMS, MPD |
| 3 | 183 | 0.59 | 0.82 | 34 | DMS |
| 4 | 176 | 0.57 | 0.81 | 30 | DMS |
| 5 | 76 | 0.39 | 0.78 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 2465 Ų buried · 58 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 3ZBG · Crystal structure of wild-type SCP2 thiolase from Leishmania mexicana at 1.85 A · 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 3ZBG · PDBe 3ZBG · UniProt E9AW84
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