MolNFT v1 · #12852 · protein

Thermolysin complexed with Z-D-alanine (benzyloxycarbonyl-D-alanine)

1KTO: “Thermolysin complexed with Z-D-alanine (benzyloxycarbonyl-D-alanine)”. X-ray diffraction, 4 ligands (PHQ, DAL, CA), 1 pocket (best druggability 0.52). MolNFT v1 #12852 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1KTO
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: PHQ, DAL, CA, ZN
Pockets: 1 · best druggability 0.52

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thermolysin (EC 3.4.24.27)	protein	316	41% helix, 17% strand	P00800

Ligands and binding sites

PHQ · benzyl chlorocarbonate · ligand · chains A
DAL · D-alanine · ligand · chains A
CA · Calcium ion · metal · 4 copies · chains A
ZN · Zinc ion · metal · 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	137	0.52	0.80	25	ZN, PHQ, DAL

Compared structures

1KTO · Thermolysin complexed with Z-D-Alanine (benzyloxycarbonyl-D-Alanine) · the same entry in another collection · chain A against A, TM-score 1.00
P00800 · AlphaFold monomer V2.0 prediction for thermolysin (P00800) · a predicted model of the same protein · 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 P00800
Elsewhere: RCSB PDB 1KTO · PDBe 1KTO · UniProt P00800

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