Research workbench

Protease inhibitors variant, cti-homolog pacifastin

Analyse Protease inhibitors variant, cti-homolog pacifastin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7SGQ
Type: protein
Length: 200 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protease inhibitor lcmi-II
UniProt: P80060
Ligands: SO4
Pockets: 2 · best druggability 0.74

Structure

x-ray diffraction · 6 distinct chains · 0% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protease inhibitor lcmi-II	protein	32	0% helix, 44% strand	P80060
B	Protease inhibitor lcmi-II	protein	33	0% helix, 42% strand	P80060
C	Protease inhibitor lcmi-II	protein	34	0% helix, 35% strand	P80060
D	Protease inhibitor lcmi-II	protein	34	0% helix, 35% strand	P80060
E	Protease inhibitor lcmi-II	protein	35	0% helix, 37% strand	P80060
F	Protease inhibitor lcmi-II	protein	32	0% helix, 25% strand	P80060

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A, D, B

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	711	0.74	0.80	63	empty
2	102	0.45	0.78	20	empty

Interfaces

11 interfaces between chains.

A–B · 457 Å² buried · 12 hydrogen bonds · protein-protein
D–E · 361 Å² buried · 7 hydrogen bonds · protein-protein
C–F · 304 Å² buried · 5 hydrogen bonds · protein-protein
E–F · 285 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 220 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 17 disulfide (disulfide).

Compared structures

7SGQ · Protease inhibitors variant, CTI-homolog pacifastin · the same entry in another collection · chain F against F, TM-score 1.00
P80060 · AlphaFold monomer V2.0 prediction for protease inhibitors (P80060) · a predicted model of the same protein · chain F against A, TM-score 0.82

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 P80060
Elsewhere: RCSB PDB 7SGQ · PDBe 7SGQ · UniProt P80060

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