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Bromopentafluorobenzene binding in the hydrophobic cavity of T4 lysozyme L99A mutant

Analyse Bromopentafluorobenzene binding in the hydrophobic cavity of T4 lysozyme L99A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3DN2
Type: protein
Length: 164 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysozyme
EC: 3.2.1.17
UniProt: P00720
Ligands: BBF, PO4
Pockets: 2 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 64% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysozyme (EC 3.2.1.17)	protein	164	64% helix, 8% strand	P00720

Ligands and binding sites

BBF · 1-bromo-2,3,4,5,6-pentafluorobenzene · ligand · chains A
PO4 · Phosphate ion · ion · 2 copies · chains A
HED · 2-hydroxyethyl disulfide · additive · 2 copies · chains A

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

Pockets

2 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	52	0.72	0.98	15	BBF
2	225	0.53	0.77	30	HED

Compared structures

3DN2 · Bromopentafluorobenzene binding in the hydrophobic cavity of T4 lysozyme L99A mutant · 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 3DN2 · PDBe 3DN2 · UniProt P00720

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