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Cu-mediated dimer of T4 lysozyme D61H/K65H/R76H/R80H by synthetic symmetrization

Analyse Cu-mediated dimer of T4 lysozyme D61H/K65H/R76H/R80H by synthetic symmetrization in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3SB6
Type: protein
Length: 328 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysozyme
EC: 3.2.1.17
UniProt: P00720
Ligands: CU, CL
Pockets: 3 · best druggability 0.54

Structure

x-ray diffraction · 1 distinct chain · 62% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Lysozyme (EC 3.2.1.17)	protein	164	62% helix, 8% strand	P00720

Ligands and binding sites

CU · Copper (II) ion · metal · 2 copies · chains A, B
CL · Chloride ion · ion · 2 copies · chains A, B

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

Pockets

3 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	253	0.54	0.76	31	CL
2	228	0.49	0.75	27	empty
3	146	0.39	0.73	20	empty

Interfaces

1 interface between chains.

A–B · 154 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

3SB6 · Cu-mediated Dimer of T4 Lysozyme D61H/K65H/R76H/R80H by Synthetic Symmetrization · 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 P00720
Elsewhere: RCSB PDB 3SB6 · PDBe 3SB6 · UniProt P00720

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