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X-ray structure of thermolysin soaked with sodium aspartate on a silicon chip

Analyse X-ray structure of thermolysin soaked with sodium aspartate on a silicon chip in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6QF3
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: ASP, CA, NA, ZN
Pockets: 1 · best druggability 0.45

Structure

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

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

Ligands and binding sites

ASP · Aspartic acid · ligand · 2 copies · chains A
CA · Calcium ion · metal · 4 copies · chains A
NA · Sodium ion · metal · 4 copies · chains A
ZN · Zinc ion · metal · chains A
EDO · 1,2-ethanediol · additive · 15 copies · chains A
P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · chains A
PGE · Triethylene glycol · additive · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	118	0.45	0.78	22	NA, EDO, ASP

Compared structures

6QF3 · X-Ray structure of Thermolysin soaked with sodium aspartate on a silicon chip · 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 6QF3 · PDBe 6QF3 · UniProt P00800

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