Research workbench

NMR structure of the mlv encapsidation signal bound to the nucleocapsid protein

Analyse NMR structure of the mlv encapsidation signal bound to the nucleocapsid protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1U6P
Type: protein + RNA
Length: 157 residues
Chains: 2
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gag polyprotein; 101-mer
UniProt: P03332
Ligands: ZN
Pockets: 3 · best druggability 0.60

Structure

solution nmr · 2 distinct chains · 5% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Gag polyprotein	protein	56	5% helix, 4% strand	P03332
B	101-mer	rna	101	—	—

Ligands and binding sites

ZN · Zinc ion · metal · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	390	0.60	0.77	27	empty
2	265	0.47	0.74	21	empty
3	172	0.39	0.73	16	empty

Interfaces

1 interface between chains.

A–B · 626 Å² buried · 16 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

1U6P · NMR Structure of the MLV encapsidation signal bound to the Nucleocapsid protein · 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 P03332
Elsewhere: RCSB PDB 1U6P · PDBe 1U6P · UniProt P03332

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