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Crystal structure of saxthrombin

Analyse Crystal structure of saxthrombin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3S69
Type: protein
Length: 234 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thrombin-like enzyme defibrase
EC: 3.4.21.-
UniProt: Q7SZE1
Ligands: CA
Pockets: 1 · best druggability 0.34

Structure

x-ray diffraction · 1 distinct chain · 10% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thrombin-like enzyme defibrase (EC 3.4.21.-)	protein	234	10% helix, 33% strand	Q7SZE1

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · 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	57	0.34	0.78	16	empty

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

3S69 · Crystal structure of saxthrombin · the same entry in another collection · chain A against A, TM-score 1.00
Q7SZE1 · AlphaFold monomer V2.0 prediction for thrombin-like enzyme saxthrombin (Q7SZE1) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q7SZE1
Elsewhere: RCSB PDB 3S69 · PDBe 3S69 · UniProt Q7SZE1

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