MolNFT v1 · #38447 · protein
Methanethiol-cys 112 inhibition complex of E. COLI ketoacyl synthase III (fabh) and coenzyme a
2GYO · 3-oxoacyl-[acyl-carrier-protein] synthase 3: “Methanethiol-cys 112 inhibition complex of E. COLI ketoacyl synthase III (fabh) and coenzyme a”. X-ray diffraction, 3 ligands (COA, MEE, SO4), 7 pockets (best druggability 0.78). MolNFT…
- PDB
- 2GYO
- Type
- protein
- Length
- 634 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-[acyl-carrier-protein] synthase 3
- EC
- 2.3.1.41
- UniProt
- P0A6R0
- Ligands
- COA, MEE, SO4
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-oxoacyl-[acyl-carrier-protein] synthase 3 (EC 2.3.1.41) | protein | 317 | 40% helix, 27% strand | P0A6R0 |
Ligands and binding sites
- COA · Coenzyme A · ligand · chains A
- MEE · Methanethiol · ligand · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, 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 | 304 | 0.78 | 0.90 | 59 | empty |
| 2 | 174 | 0.66 | 0.85 | 36 | COA, MEE |
| 3 | 135 | 0.61 | 0.85 | 30 | empty |
| 4 | 103 | 0.40 | 0.76 | 21 | SO4 |
| 5 | 110 | 0.40 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2317 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2GYO · Methanethiol-Cys 112 Inhibition Complex of E. Coli Ketoacyl Synthase III (FabH) and… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A6R0 · AlphaFold monomer V2.0 prediction for 3-oxoacyl-[acyl-carrier- protein] synthase 3… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P0A6R0
- Elsewhere: RCSB PDB 2GYO · PDBe 2GYO · UniProt P0A6R0
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