MolNFT v1 · #34084 · protein

Monoclinic hen egg-white lysozyme crystallized at 313K

2D4K: “Monoclinic hen egg-white lysozyme crystallized at 313K”. X-ray diffraction, 2 ligands (NA, CL), 3 pockets (best druggability 0.33). MolNFT v1 #34084 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2D4K
Type: protein
Length: 258 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysozyme C
EC: 3.2.1.17
UniProt: P00698
Ligands: NA, CL
Pockets: 3 · best druggability 0.33

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, N	Lysozyme C (EC 3.2.1.17)	protein	129	43% helix, 11% strand	P00698

Ligands and binding sites

NA · Sodium ion · metal · 2 copies · chains A, N
CL · Chloride ion · ion · 4 copies · chains A, N

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

Pockets

3 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	73	0.33	0.75	18	empty
2	69	0.32	0.75	17	CL
3	67	0.30	0.74	18	empty

Interfaces

1 interface between chains.

A–N · 285 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

2D4K · Monoclinic hen egg-white lysozyme crystallized at 313K · 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 2D4K · PDBe 2D4K · UniProt P00698

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