Research workbench
Crystal structure of peptidoglycan deacetylase (HP0310) with zinc from helicobacter pylori
Analyse Crystal structure of peptidoglycan deacetylase (HP0310) with zinc from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LY4
- Type
- protein
- Length
- 1,160 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidoglycan deacetylase
- UniProt
- B5ZA76
- Ligands
- ZN
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Peptidoglycan deacetylase | protein | 290 | 47% helix, 16% strand | B5ZA76 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 279 | 0.81 | 0.92 | 39 | empty |
| 2 | 100 | 0.55 | 0.84 | 20 | empty |
| 3 | 116 | 0.54 | 0.82 | 18 | empty |
| 4 | 103 | 0.54 | 0.83 | 18 | empty |
| 5 | 117 | 0.52 | 0.81 | 19 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2372 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2368 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 2361 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 2361 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 4LY4 · Crystal structure of peptidoglycan deacetylase (HP0310) with Zinc from Helicobacter pylori · the same entry in another collection · chain A against A, TM-score 1.00
- B5ZA76 · AlphaFold monomer V2.0 prediction for peptidoglycan deacetylase (B5ZA76) · 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 B5ZA76
- Elsewhere: RCSB PDB 4LY4 · PDBe 4LY4 · UniProt B5ZA76
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