MolNFT v1 · #66148 · protein

Complex of a vesicular stomatitis virus empty capsid with the nucleocapsid-binding domain of the phosphoprotein

3HHW: “Complex of a vesicular stomatitis virus empty capsid with the nucleocapsid-binding domain of the…”. X-ray diffraction, 20 pockets (best druggability 0.81). MolNFT v1 #66148 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 3HHW
Type: protein
Length: 2,470 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphoprotein; Nucleoprotein
UniProt: P04880, Q77E03
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Phosphoprotein	protein	73	41% helix, 14% strand	P04880
K, L, M, N, O	Nucleoprotein	protein	421	44% helix, 6% strand	Q77E03

Ligands and binding sites

TAR · D(-)-tartaric acid · additive · 6 copies · chains K, O, C, M

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

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	852	0.81	0.84	95	TAR
2	840	0.80	0.83	100	TAR
3	784	0.79	0.82	74	empty
4	678	0.76	0.82	60	empty
5	716	0.69	0.76	86	empty

Interfaces

20 interfaces between chains.

K–O · 2724 Å² buried · 26 hydrogen bonds · protein-protein
M–N · 2668 Å² buried · 25 hydrogen bonds · protein-protein
K–L · 2600 Å² buried · 22 hydrogen bonds · protein-protein
L–M · 2511 Å² buried · 19 hydrogen bonds · protein-protein
D–N · 836 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 modified (engineered).

Compared structures

3HHW · Complex of a vesicular stomatitis virus empty capsid with the nucleocapsid-binding domain… · 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 P04880
Every structure of UniProt Q77E03
Elsewhere: RCSB PDB 3HHW · PDBe 3HHW · UniProt P04880 · UniProt Q77E03

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