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Structure of Tetragonal Lysozyme in complex with Iodine solved by UWO Students

Analyse Structure of Tetragonal Lysozyme in complex with Iodine solved by UWO Students in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5DL9
Type: protein
Length: 129 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.38
Source: Gallus gallus
Molecule: Lysozyme C
EC: 3.2.1.17
UniProt: P00698
Ligands: IOD
Pockets: 1 · best druggability 0.33

Structure

x-ray diffraction · resolution 1.38 · 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

IOD · Iodide ion · ion · 4 copies · chains A
EDO · 1,2-ethanediol · additive · 9 copies · chains A
ACT · Acetate ion · 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	63	0.33	0.77	18	EDO, ACT

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5DL9 · Structure of tetragonal lysozyme in complex with iodine solved by uwo students · 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 5DL9 · PDBe 5DL9 · UniProt P00698

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