MolNFT v1 · #3999 · protein
Bacteriophage lambda lysozyme complexed with a chitohexasacharide
1D9U: “Bacteriophage lambda lysozyme complexed with a chitohexasacharide”. X-ray diffraction, 3 ligands (NAG, NDG, SO4), 3 pockets (best druggability 0.65). MolNFT v1 #3999 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1D9U
- Type
- protein
- Length
- 308 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriophage lambda lysozyme
- EC
- 3.2.1.17
- UniProt
- P03706
- Ligands
- NAG, NDG, SO4
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bacteriophage lambda lysozyme (EC 3.2.1.17) | protein | 154 | 38% helix, 8% strand | P03706 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 463 | 0.65 | 0.77 | 36 | NAG |
| 2 | 270 | 0.54 | 0.76 | 32 | NAG |
| 3 | 61 | 0.41 | 0.81 | 17 | SO4 |
Interfaces
1 interface between chains.
- A–B · 357 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1D9U · Bacteriophage lambda lysozyme complexed with a chitohexasacharide · 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 P03706
- Elsewhere: RCSB PDB 1D9U · PDBe 1D9U · UniProt P03706
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.