MolNFT v1 · #14141 · protein
Structural changes of the active site cleft and different saccharide binding modes in human lysozyme co-crystallized with hexa-N-acetyl- chitohexaose at pH 4.0
1LZS: “Structural changes of the active site cleft and different saccharide binding modes in human lysozyme…”. X-ray diffraction, 2 ligands (NAG, NA), 3 pockets (best druggability 0.53). MolNFT v1 #14141 on GenesisL1: 3D structure, binding…
- PDB
- 1LZS
- Type
- protein
- Length
- 260 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human lysozyme
- EC
- 3.2.1.17
- UniProt
- P00695
- Ligands
- NAG, NA
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Human lysozyme (EC 3.2.1.17) | protein | 130 | 38% helix, 12% strand | P00695 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
- NA · Sodium ion · metal · 2 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.53 | 0.82 | 31 | empty |
| 2 | 77 | 0.36 | 0.76 | 17 | NAG |
| 3 | 69 | 0.33 | 0.76 | 17 | NAG |
Interfaces
1 interface between chains.
- A–B · 393 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1LZS · Structural changes of the active site cleft and different saccharide binding modes in… · 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 P00695
- Elsewhere: RCSB PDB 1LZS · PDBe 1LZS · UniProt P00695
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