MolNFT v1 · #126193 · protein

Hen egg white lysozyme soaked with [H2IND][TRANS-RUCL4(DMSO)(HIND)]

5LVJ · Lysozyme C: “Hen egg white lysozyme soaked with [H2IND][TRANS-RUCL4(DMSO)(HIND)]”. X-ray diffraction, 3 ligands (NA, RU, CL), 1 pocket (best druggability 0.35). MolNFT v1 #126193 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5LVJ
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: NA, RU, CL
Pockets: 1 · best druggability 0.35

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

NA · Sodium ion · metal · chains A
RU · Ruthenium ion · metal · chains A
CL · Chloride ion · ion · 8 copies · chains A
ACT · Acetate ion · additive · 4 copies · chains A
GOL · Glycerol · additive · 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	78	0.35	0.76	20	CL, ACT

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5LVJ · Hen Egg White Lysozyme co-crystallized with [H2Ind][trans-RuCl4(DMSO)(HInd)] · 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 5LVJ · PDBe 5LVJ · UniProt P00698

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