MolNFT v1 · #116814 · protein

Thermolysin in complex with inhibitor.

5DPE: “Thermolysin in complex with inhibitor.”. X-ray diffraction, 3 ligands (5H8, CA, ZN), 1 pocket (best druggability 0.47). MolNFT v1 #116814 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5DPE
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: 5H8, CA, ZN
Pockets: 1 · best druggability 0.47

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Thermolysin (EC 3.4.24.27)	protein	316	42% helix, 18% strand	P00800

Ligands and binding sites

5H8 · N-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucyl-3-methyl-L-valine · ligand · chains E
CA · Calcium ion · metal · 4 copies · chains E
ZN · Zinc ion · metal · chains E
DMS · Dimethyl sulfoxide · additive · 4 copies · chains E
GOL · Glycerol · additive · 3 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	131	0.47	0.78	25	5H8, GOL

Compared structures

5DPE · Thermolysin in complex with inhibitor. · 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 5DPE · PDBe 5DPE · UniProt P00800

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