Research workbench

Crystal structure of marburg virus nucleoprotein core domain bound to VP35 regulation peptide

Analyse Crystal structure of marburg virus nucleoprotein core domain bound to VP35… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5F5O
Type: protein
Length: 1,028 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoprotein; Peptide from polymerase cofactor VP35
UniProt: Q6UY69, Q6UY68
Ligands: SO4
Pockets: 6 · best druggability 0.74

Structure

x-ray diffraction · 6 distinct chains · 61% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nucleoprotein	protein	315	62% helix, 5% strand	Q6UY69
B	Peptide from polymerase cofactor VP35	protein	26	50% helix, 0% strand	Q6UY68
C	Nucleoprotein	protein	318	62% helix, 6% strand	Q6UY69
D	Peptide from polymerase cofactor VP35	protein	27	67% helix, 0% strand	Q6UY68
E	Nucleoprotein	protein	315	62% helix, 6% strand	Q6UY69
F	Peptide from polymerase cofactor VP35	protein	27	56% helix, 0% strand	Q6UY68

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A, C

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	840	0.74	0.79	77	empty
2	769	0.73	0.79	82	empty
3	68	0.44	0.82	15	empty
4	86	0.36	0.76	23	empty
5	65	0.27	0.73	16	SO4

Interfaces

7 interfaces between chains.

E–F · 1142 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 1048 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 1024 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 835 Å² buried · 11 hydrogen bonds · protein-protein
A–E · 380 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5F5O · Crystal structure of Marburg virus nucleoprotein core domain bound to VP35 regulation… · 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 Q6UY69
Every structure of UniProt Q6UY68
Elsewhere: RCSB PDB 5F5O · PDBe 5F5O · UniProt Q6UY69 · UniProt Q6UY68

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