MolNFT v1 · #118557 · protein

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

5F5O: “Crystal structure of marburg virus nucleoprotein core domain bound to VP35 regulation peptide”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.74). MolNFT v1 #118557 on GenesisL1: 3D structure, binding sites and…

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

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