MolNFT v1 · #176369 · protein + RNA

Influenza H5N1 nucleoprotein (truncated) in complex with nucleotides

7DKG: “Influenza H5N1 nucleoprotein (truncated) in complex with nucleotides”. X-ray diffraction, 14 pockets (best druggability 0.77). MolNFT v1 #176369 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7DKG
Type: protein + RNA
Length: 805 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoprotein; RNA (5'-R(P*(OMU)P*(OMU)P*(OMU))-3')
UniProt: Q9PX50
Pockets: 14 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 50% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nucleoprotein	protein	393	51% helix, 8% strand	Q9PX50
B	Nucleoprotein	protein	409	49% helix, 9% strand	Q9PX50
C	RNA (5'-R(P(OMU)P(OMU)P*(OMU))-3')	rna	3	—	—

Pockets

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	906	0.77	0.80	96	empty
2	136	0.65	0.88	23	empty
3	260	0.56	0.78	30	empty
4	149	0.54	0.80	19	empty
5	269	0.51	0.74	34	empty

Interfaces

2 interfaces between chains.

A–B · 658 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 562 Å² buried · 12 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 3 modified (nucleotide modification).

Compared structures

7DKG · Influenza H5N1 nucleoprotein (truncated) in complex with nucleotides · 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 Q9PX50
Elsewhere: RCSB PDB 7DKG · PDBe 7DKG · UniProt Q9PX50

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