MolNFT v1 · #123340 · protein

Spin-labeled T4 lysozyme construct T151V1

5JGZ · Endolysin: “Spin-labeled T4 lysozyme construct T151V1”. X-ray diffraction, 4 ligands (V1A, K, CL), 1 pocket (best druggability 0.54). MolNFT v1 #123340 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5JGZ
Type: protein
Length: 163 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endolysin
EC: 3.2.1.17
UniProt: P00720
Ligands: V1A, K, CL, PO4
Pockets: 1 · best druggability 0.54

Structure

x-ray diffraction · 1 distinct chain · 63% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Endolysin (EC 3.2.1.17)	protein	163	63% helix, 8% strand	P00720

Ligands and binding sites

V1A · S-(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-imidazol-4-yl) methanesulfonothioate · ligand · chains A
K · Potassium ion · metal · chains A
CL · Chloride ion · ion · chains A
PO4 · Phosphate ion · ion · chains A
HEZ · Hexane-1,6-diol · additive · 2 copies · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	230	0.54	0.77	29	K, HEZ

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

5JGZ · Spin-Labeled T4 Lysozyme Construct T151V1 · 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 5JGZ · PDBe 5JGZ · UniProt P00720

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