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New crystal structure of yeast DDI1 aspartyl protease reveals substrate engagement mode

Analyse New crystal structure of yeast DDI1 aspartyl protease reveals substrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4Z2Z
Type: protein
Length: 261 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA damage-inducible protein 1
UniProt: P40087
Pockets: 1 · best druggability 0.32

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA damage-inducible protein 1	protein	123	15% helix, 42% strand	P40087
B	DNA damage-inducible protein 1	protein	138	11% helix, 41% strand	P40087

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	75	0.32	0.74	19	empty

Interfaces

1 interface between chains.

A–B · 1136 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

4Z2Z · New crystal structure of yeast Ddi1 aspartyl protease reveals substrate engagement mode · the same entry in another collection · chain A against A, TM-score 1.00
P40087 · AlphaFold monomer V2.0 prediction for DNA damage-inducible protein 1 (P40087) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 P40087
Elsewhere: RCSB PDB 4Z2Z · PDBe 4Z2Z · UniProt P40087

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