MolNFT v1 · #45055 · protein + RNA

Solution NMR structure of the U5-primer binding site (U5-pbs) domain of murine leukemia virus RNA genome bound to the retroviral nucleocapsid protein

2MQV · Nucleocapsid protein P10: “Solution NMR structure of the U5-primer binding site (U5-pbs) domain of murine leukemia virus RNA genome…”. Solution nmr, 1 ligand (ZN), 2 pockets (best druggability 0.68). MolNFT v1 #45055 on GenesisL1…

PDB: 2MQV
Type: protein + RNA
Length: 124 residues
Chains: 2
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleocapsid protein P10; RNA (68-mer)
UniProt: P03355
Ligands: ZN
Pockets: 2 · best druggability 0.68

Structure

solution nmr · 2 distinct chains · 11% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nucleocapsid protein P10	protein	56	11% helix, 4% strand	P03355
B	RNA (68-mer)	rna	68	—	—

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

2 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	633	0.68	0.78	40	empty
2	281	0.48	0.73	24	empty

Interfaces

1 interface between chains.

A–B · 1097 Å² buried · 35 hydrogen bonds · protein-nucleic

Compared structures

2MQV · Solution NMR structure of the U5-primer binding site (U5-PBS) domain of murine leukemia… · 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 P03355
Elsewhere: RCSB PDB 2MQV · PDBe 2MQV · UniProt P03355

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