MolNFT v1 · #123592 · protein
Bdellovibrio bacteriovorus peptidoglycan deacetylase BD3279
5JP6 · Putative polysaccharide deacetylase: “Bdellovibrio bacteriovorus peptidoglycan deacetylase BD3279”. X-ray diffraction, 2 ligands (ZN, MG), 2 pockets (best druggability 0.76). MolNFT v1 #123592 on GenesisL1: 3D structure, binding…
- PDB
- 5JP6
- Type
- protein
- Length
- 339 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative polysaccharide deacetylase
- EC
- 3.5.1.-
- UniProt
- Q6MI90
- Ligands
- ZN, MG
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative polysaccharide deacetylase (EC 3.5.1.-) | protein | 339 | 52% helix, 12% strand | Q6MI90 |
Ligands and binding sites
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 | 458 | 0.76 | 0.85 | 47 | empty |
| 2 | 55 | 0.36 | 0.78 | 16 | empty |
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 5JP6 · Bdellovibrio bacteriovorus peptidoglycan deacetylase Bd3279 · 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 Q6MI90
- Elsewhere: RCSB PDB 5JP6 · PDBe 5JP6 · UniProt Q6MI90
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