Research workbench

Ebola virus VP30 ctd bound to nucleoprotein

Analyse Ebola virus VP30 ctd bound to nucleoprotein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5T3T
Type: protein
Length: 1,363 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fusion protein of nucleoprotein and minor nucleoprotein VP30
UniProt: P18272, Q05323
Ligands: SO4
Pockets: 12 · best druggability 0.80

Structure

x-ray diffraction · 6 distinct chains · 65% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fusion protein of nucleoprotein and minor nucleoprotein VP30	protein	139	64% helix, 0% strand	P18272, Q05323
B, D, I	Fusion protein of nucleoprotein and minor nucleoprotein VP30	protein	136	67% helix, 0% strand	P18272, Q05323
C, F, H	Fusion protein of nucleoprotein and minor nucleoprotein VP30	protein	136	65% helix, 0% strand	P18272, Q05323
E	Fusion protein of nucleoprotein and minor nucleoprotein VP30	protein	137	65% helix, 0% strand	P18272, Q05323
G	Fusion protein of nucleoprotein and minor nucleoprotein VP30	protein	136	65% helix, 0% strand	P18272, Q05323
J	Fusion protein of nucleoprotein and minor nucleoprotein VP30	protein	135	64% helix, 0% strand	P18272, Q05323

Ligands and binding sites

SO4 · Sulfate ion · ion · 27 copies · chains A, B, C, D, E, F, G, H, I, J

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

Pockets

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	841	0.80	0.83	108	SO4
2	372	0.59	0.76	41	SO4
3	366	0.59	0.76	44	SO4
4	160	0.59	0.82	18	empty
5	333	0.55	0.75	44	SO4

Interfaces

18 interfaces between chains.

C–D · 3067 Å² buried · 28 hydrogen bonds · protein-protein
E–F · 3053 Å² buried · 28 hydrogen bonds · protein-protein
I–J · 3017 Å² buried · 31 hydrogen bonds · protein-protein
A–B · 2998 Å² buried · 31 hydrogen bonds · protein-protein
G–H · 2919 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

5T3T · Ebola virus VP30 CTD bound to nucleoprotein · 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 P18272
Every structure of UniProt Q05323
Elsewhere: RCSB PDB 5T3T · PDBe 5T3T · UniProt P18272 · UniProt Q05323

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