MolNFT v1 · #136959 · protein

Pekin duck egg lysozyme isoform III (del-III), cubic form

5V94: “Pekin duck egg lysozyme isoform III (del-III), cubic form”. X-ray diffraction, 1 ligand (PO4), 2 pockets (best druggability 0.54). MolNFT v1 #136959 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5V94
Type: protein
Length: 258 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysozyme isoform III
EC: 3.2.1.18
UniProt: U3J0P1
Ligands: PO4
Pockets: 2 · best druggability 0.54

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Lysozyme isoform III (EC 3.2.1.18)	protein	129	42% helix, 11% strand	U3J0P1

Ligands and binding sites

PO4 · Phosphate ion · ion · 7 copies · chains A, B
MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	245	0.54	0.76	23	empty
2	56	0.30	0.75	13	TRS

Interfaces

1 interface between chains.

A–B · 290 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5V94 · Pekin duck egg lysozyme isoform III (DEL-III), cubic form · 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 U3J0P1
Elsewhere: RCSB PDB 5V94 · PDBe 5V94 · UniProt U3J0P1

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