MolNFT v1 · #146166 · protein
Pekin duck egg lysozyme isoform II (del-II)
6D9I: “Pekin duck egg lysozyme isoform II (del-II)”. X-ray diffraction, 2 ligands (MG, CL), 2 pockets (best druggability 0.67). MolNFT v1 #146166 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6D9I
- Type
- protein
- Length
- 258 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme
- EC
- 3.2.1.17
- UniProt
- U3J0P1
- Ligands
- MG, CL
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lysozyme (EC 3.2.1.17) | protein | 129 | 42% helix, 11% strand | U3J0P1 |
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 | 332 | 0.67 | 0.82 | 32 | empty |
| 2 | 107 | 0.44 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 462 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6D9I · Pekin duck egg lysozyme isoform II (DEL-II) · the same entry in another collection · chain B against B, 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 U3J0P1
- Elsewhere: RCSB PDB 6D9I · PDBe 6D9I · UniProt U3J0P1
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