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Crystal structure of a retropepsin-like aspartic protease from rickettsia conorii

Analyse Crystal structure of a retropepsin-like aspartic protease from rickettsia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5C9D
Type: protein
Length: 235 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aprick protease
UniProt: Q92FY8
Ligands: NA
Pockets: 2 · best druggability 0.43

Structure

x-ray diffraction · 2 distinct chains · 10% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Aprick protease	protein	115	11% helix, 50% strand	Q92FY8
B	Aprick protease	protein	120	8% helix, 45% strand	Q92FY8

Ligands and binding sites

NA · Sodium ion · metal · chains A, 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	102	0.43	0.77	15	empty
2	62	0.37	0.78	18	empty

Interfaces

1 interface between chains.

A–B · 808 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

5C9D · Crystal structure of a retropepsin-like aspartic protease from Rickettsia conorii · 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 Q92FY8
Elsewhere: RCSB PDB 5C9D · PDBe 5C9D · UniProt Q92FY8

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