MolNFT v1 · #146726 · protein
Streptococcus pyogenes deacetylase ppld in complex with acetate
6DQ3 · Polysaccharide deacetylase: “Streptococcus pyogenes deacetylase ppld in complex with acetate”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.64). MolNFT v1 #146726 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6DQ3
- Type
- protein
- Length
- 453 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polysaccharide deacetylase
- UniProt
- J7M3C9
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polysaccharide deacetylase | protein | 227 | 42% helix, 21% strand | J7M3C9 |
| B | Polysaccharide deacetylase | protein | 226 | 42% helix, 21% strand | J7M3C9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B
- ACT · Acetate ion · additive · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
- IMD · Imidazole · additive · chains B
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 | 469 | 0.64 | 0.77 | 51 | empty |
| 2 | 54 | 0.32 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 694 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 6DQ3 · Streptococcus pyogenes deacetylase PplD in complex with acetate · 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 J7M3C9
- Elsewhere: RCSB PDB 6DQ3 · PDBe 6DQ3 · UniProt J7M3C9
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