Research workbench

Bobwhite quail lysozyme with nitrate

Analyse Bobwhite quail lysozyme with nitrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1DKK
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: P00700
Ligands: NO3
Pockets: 2 · best druggability 0.33

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Lysozyme (EC 3.2.1.17)	protein	129	41% helix, 11% strand	P00700

Ligands and binding sites

NO3 · Nitrate ion · ion · 4 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	68	0.33	0.75	14	empty
2	57	0.29	0.75	17	NO3

Interfaces

1 interface between chains.

A–B · 329 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

1DKK · Bobwhite quail lysozyme with nitrate · the same entry in another collection · chain A against A, TM-score 1.00
P00700 · AlphaFold monomer V2.0 prediction for lysozyme C (P00700) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P00700
Elsewhere: RCSB PDB 1DKK · PDBe 1DKK · UniProt P00700

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