MolNFT v1 · #126187 · protein

Thermolysin in complex with inhibitor (JC67)

5LVD: “Thermolysin in complex with inhibitor (JC67)”. X-ray diffraction, 3 ligands (79F, CA, ZN), 1 pocket (best druggability 0.46). MolNFT v1 #126187 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5LVD
Type: protein
Length: 316 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thermolysin
EC: 3.4.24.27
UniProt: P00800
Ligands: 79F, CA, ZN
Pockets: 1 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Thermolysin (EC 3.4.24.27)	protein	316	41% helix, 18% strand	P00800

Ligands and binding sites

79F · (2~{S})-4-methyl-2-[[(2~{S})-3-oxidanyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl) phosphoryl]amino]propanoyl]amino]pentanoic acid · ligand · chains E
CA · Calcium ion · metal · 4 copies · chains E
ZN · Zinc ion · metal · chains E
GOL · Glycerol · additive · 2 copies · chains E
DMS · Dimethyl sulfoxide · additive · 2 copies · chains E

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	141	0.46	0.77	24	GOL, 79F

Compared structures

5LVD · Thermolysin in complex with inhibitor (JC67) · the same entry in another collection · chain E against E, 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 P00800
Elsewhere: RCSB PDB 5LVD · PDBe 5LVD · UniProt P00800

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.