MolNFT v1 · #78513 · protein

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

3SB7: “Cu-mediated trimer of T4 lysozyme D61H/K65H/R76H/R80H by synthetic symmetrization”. X-ray diffraction, 1 ligand (CU), 3 pockets (best druggability 0.77). MolNFT v1 #78513 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3SB7
Type: protein
Length: 325 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
Pockets: 3 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 61% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysozyme (EC 3.2.1.17)	protein	163	61% helix, 10% strand	P00720
B	Lysozyme (EC 3.2.1.17)	protein	162	61% helix, 10% strand	P00720

Ligands and binding sites

CU · Copper (II) ion · metal · chains B
GOL · Glycerol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	775	0.77	0.81	63	empty
2	138	0.53	0.80	24	empty
3	70	0.48	0.83	17	empty

Interfaces

1 interface between chains.

A–B · 966 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

3SB7 · Cu-mediated Trimer 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 3SB7 · PDBe 3SB7 · UniProt P00720

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