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Thermolysin in complex with JC114 (PEG400 cryo protectant)

Analyse Thermolysin in complex with JC114 (PEG400 cryo protectant) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5L8P
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: 6MG, CA, ZN
Pockets: 2 · best druggability 0.50

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

6MG · N~2~-[(R)-({[(benzyloxy)carbonyl]amino}methyl) (hydroxy)phosphoryl]-N-[(2S)-2,3,3-trimethylbutyl]-L-leucinamide · ligand · chains E
CA · Calcium ion · metal · 4 copies · chains E
ZN · Zinc ion · metal · 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

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	139	0.50	0.79	23	6MG
2	56	0.30	0.75	13	empty

Compared structures

5L8P · Thermolysin in complex with JC114 (PEG400 cryo protectant) · 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 5L8P · PDBe 5L8P · UniProt P00800

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