MolNFT v1 · #115968 · protein
The complex structure of vink with vinl
5CZD · Malonyl-CoA-[acyl-carrier-protein] transacylase: “The complex structure of vink with vinl”. X-ray diffraction, 2 ligands (PNS, 1N2), 2 pockets (best druggability 0.81). MolNFT v1 #115968 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5CZD
- Type
- protein
- Length
- 378 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malonyl-CoA-[acyl-carrier-protein] transacylase; Acyl-carrier-protein
- UniProt
- Q76KY5, Q76KY4
- Ligands
- PNS, 1N2
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Malonyl-CoA-[acyl-carrier-protein] transacylase | protein | 301 | 50% helix, 18% strand | Q76KY5 |
| B | Acyl-carrier-protein | protein | 77 | 52% helix, 0% strand | Q76KY4 |
Ligands and binding sites
- PNS · 4'-phosphopantetheine · ligand · chains A, B
- 1N2 · 1,1'-ethane-1,2-diyldipyrrolidine-2,5-dione · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 822 | 0.81 | 0.84 | 81 | PNS, 1N2 |
| 2 | 79 | 0.36 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 702 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor, 1 covalent (phosphopantetheinylation, covalent ligand).
Compared structures
- 5CZD · The complex structure of VinK with VinL · 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 Q76KY5
- Every structure of UniProt Q76KY4
- Elsewhere: RCSB PDB 5CZD · PDBe 5CZD · UniProt Q76KY5 · UniProt Q76KY4
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