MolNFT v1 · #140758 · protein

Crystal structure of cross-linked tetragonal hen egg white lysozyme soaked with 10 mm rose bengal and 10MM H2PTCL6

5YKY · Lysozyme C: “Crystal structure of cross-linked tetragonal hen egg white lysozyme soaked with 10 mm rose bengal and 10MM…”. X-ray diffraction, 3 ligands (PT, NA, CL), 1 pocket (best druggability 0.31). MolNFT v1 #140758 on GenesisL1…

PDB: 5YKY
Type: protein
Length: 129 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysozyme C
EC: 3.2.1.17
UniProt: P00698
Ligands: PT, NA, CL
Pockets: 1 · best druggability 0.31

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysozyme C (EC 3.2.1.17)	protein	129	41% helix, 11% strand	P00698

Ligands and binding sites

PT · Platinum (II) ion · metal · 2 copies · chains A
NA · Sodium ion · metal · chains A
CL · Chloride ion · ion · 12 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	63	0.31	0.75	18	empty

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5YKY · Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 mM… · 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 P00698
Elsewhere: RCSB PDB 5YKY · PDBe 5YKY · UniProt P00698

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