MolNFT v1 · #150938 · protein
Structure of peptidoglycan deacetylase pdac from bacillus subtilis - mutant D285S
6H8N · Peptidoglycan-N-acetylmuramic acid deacetylase pdac: “Structure of peptidoglycan deacetylase pdac from bacillus subtilis - mutant D285S”. X-ray diffraction, 2 ligands (ZN, PO4), 2 pockets (best druggability 0.78). MolNFT v1 #150938…
- PDB
- 6H8N
- Type
- protein
- Length
- 408 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidoglycan-N-acetylmuramic acid deacetylase pdac
- EC
- 3.5.1.-
- UniProt
- O34798
- Ligands
- ZN, PO4
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan-N-acetylmuramic acid deacetylase pdac (EC 3.5.1.-) | protein | 202 | 53% helix, 13% strand | O34798 |
| B | Peptidoglycan-N-acetylmuramic acid deacetylase pdac (EC 3.5.1.-) | protein | 206 | 51% helix, 13% strand | O34798 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, 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 | 1006 | 0.78 | 0.80 | 73 | GOL |
| 2 | 96 | 0.45 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1486 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6H8N · Structure of peptidoglycan deacetylase PdaC from Bacillus subtilis - mutant D285S · the same entry in another collection · chain A against A, TM-score 1.00
- O34798 · AlphaFold monomer V2.0 prediction for peptidoglycan-N-acetylmuramic acid deacetylase pdac… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 O34798
- Elsewhere: RCSB PDB 6H8N · PDBe 6H8N · UniProt O34798
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