Research workbench

Crystal structure of retroviral protease-like domain of DDI1 from leishmania major

Analyse Crystal structure of retroviral protease-like domain of DDI1 from leishmania… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YS4
Type: protein
Length: 698 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-damage inducible protein DDI1-like protein
UniProt: E9AC52
Pockets: 6 · best druggability 0.46

Structure

x-ray diffraction · 6 distinct chains · 15% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-damage inducible protein DDI1-like protein	protein	120	15% helix, 44% strand	E9AC52
B	DNA-damage inducible protein DDI1-like protein	protein	119	16% helix, 46% strand	E9AC52
C	DNA-damage inducible protein DDI1-like protein	protein	117	15% helix, 46% strand	E9AC52
D	DNA-damage inducible protein DDI1-like protein	protein	115	16% helix, 46% strand	E9AC52
E	DNA-damage inducible protein DDI1-like protein	protein	112	17% helix, 46% strand	E9AC52
F	DNA-damage inducible protein DDI1-like protein	protein	115	14% helix, 46% strand	E9AC52

Pockets

6 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	196	0.46	0.75	27	empty
2	188	0.44	0.73	33	empty
3	96	0.34	0.73	17	empty
4	50	0.31	0.77	21	empty
5	66	0.31	0.74	16	empty

Interfaces

8 interfaces between chains.

B–C · 1196 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 1141 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 1066 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 621 Å² buried · 12 hydrogen bonds · protein-protein
C–E · 473 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5YS4 · Crystal structure of retroviral protease-like domain of Ddi1 from Leishmania major · 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 E9AC52
Elsewhere: RCSB PDB 5YS4 · PDBe 5YS4 · UniProt E9AC52

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.