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Crystal structure of mt-SP1 in complex with benzamidine

Analyse Crystal structure of mt-SP1 in complex with benzamidine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3P8G
Type: protein
Length: 241 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ST14 protein
EC: 3.4.21.109
UniProt: Q8WVC1
Ligands: BEN, GSH, SO4
Pockets: 1 · best druggability 0.41

Structure

x-ray diffraction · 1 distinct chain · 10% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ST14 protein (EC 3.4.21.109)	protein	241	10% helix, 36% strand	Q8WVC1

Ligands and binding sites

BEN · Benzamidine · ligand · chains A
GSH · Glutathione · ligand · chains A
SO4 · Sulfate ion · ion · 3 copies · chains A
EDO · 1,2-ethanediol · additive · 4 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	144	0.41	0.75	36	SO4, BEN

Modifications

Observed in the structure: 3 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

3P8G · Crystal Structure of MT-SP1 in complex with benzamidine · the same entry in another collection · 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 Q8WVC1
Elsewhere: RCSB PDB 3P8G · PDBe 3P8G · UniProt Q8WVC1

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