Research workbench

Crystal structure of the S. cerevisiae SKI2-3-8 complex

Analyse Crystal structure of the S. cerevisiae SKI2-3-8 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4BUJ
Type: protein
Length: 6,013 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antiviral helicase SKI2; Superkiller protein 3; Antiviral protein SKI8
EC: 3.6.4.13
UniProt: P35207, P17883, Q02793
Ligands: SO4
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 8 distinct chains · 49% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Antiviral helicase SKI2 (EC 3.6.4.13)	protein	903	45% helix, 12% strand	P35207
B	Superkiller protein 3	protein	1367	77% helix, 0% strand	P17883
C	Antiviral protein SKI8	protein	392	4% helix, 53% strand	Q02793
D	Antiviral protein SKI8	protein	381	2% helix, 50% strand	Q02793
E	Antiviral helicase SKI2 (EC 3.6.4.13)	protein	881	46% helix, 11% strand	P35207
F	Superkiller protein 3	protein	1351	76% helix, 0% strand	P17883
G	Antiviral protein SKI8	protein	387	4% helix, 51% strand	Q02793
H	Antiviral protein SKI8	protein	351	2% helix, 55% strand	Q02793

Ligands and binding sites

SO4 · Sulfate ion · ion · 20 copies · chains A, B, C, D, E, G, F, H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1025	0.86	0.87	98	SO4
2	703	0.85	0.89	84	SO4
3	1197	0.84	0.86	126	SO4
4	1143	0.82	0.84	114	SO4
5	620	0.79	0.85	58	SO4

Interfaces

17 interfaces between chains.

A–B · 7764 Å² buried · 59 hydrogen bonds · protein-protein
E–F · 6758 Å² buried · 51 hydrogen bonds · protein-protein
F–G · 2268 Å² buried · 23 hydrogen bonds · protein-protein
B–C · 2139 Å² buried · 25 hydrogen bonds · protein-protein
A–C · 2098 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

4BUJ · Crystal structure of the S. cerevisiae Ski2-3-8 complex · the same entry in another collection · chain H against H, TM-score 1.00
Q02793 · AlphaFold monomer V2.0 prediction for antiviral protein SKI8 (Q02793) · a predicted model of the same protein · chain H against A, TM-score 0.98
P35207 · AlphaFold monomer V2.0 prediction for antiviral helicase SKI2 (P35207) · a predicted model of the same protein · chain E against A, TM-score 0.97

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 P35207
Every structure of UniProt P17883
Every structure of UniProt Q02793
Elsewhere: RCSB PDB 4BUJ · PDBe 4BUJ · UniProt P35207 · UniProt P17883 · UniProt Q02793

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