MolNFT v1 · #141819 · protein
The structure of dszs acyltransferase with carrier protein
5ZK4 · Disd protein: “The structure of dszs acyltransferase with carrier protein”. X-ray diffraction, 2 ligands (9EF, SO4), 12 pockets (best druggability 0.73). MolNFT v1 #141819 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5ZK4
- Type
- protein
- Length
- 720 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Disd protein; Disa protein
- UniProt
- Q4U443, Q4U447
- Ligands
- 9EF, SO4
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Disd protein | protein | 287 | 51% helix, 15% strand | Q4U443 |
| C, D | Disa protein | protein | 73 | 64% helix, 0% strand | Q4U447 |
Ligands and binding sites
- 9EF · N-[2-(acetylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide · ligand · 2 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 474 | 0.73 | 0.82 | 57 | SO4, 9EF |
| 2 | 502 | 0.71 | 0.81 | 56 | SO4, 9EF |
| 3 | 62 | 0.58 | 0.90 | 17 | empty |
| 4 | 383 | 0.57 | 0.75 | 46 | SO4 |
| 5 | 136 | 0.49 | 0.78 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 792 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 670 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 654 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 603 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 602 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5ZK4 · The structure of DSZS acyltransferase with carrier protein · 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 Q4U443
- Every structure of UniProt Q4U447
- Elsewhere: RCSB PDB 5ZK4 · PDBe 5ZK4 · UniProt Q4U443 · UniProt Q4U447
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