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Structure of RNA-bound decameric hmpv nucleoprotein

Analyse Structure of RNA-bound decameric hmpv nucleoprotein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5FVC
Type: protein + RNA
Length: 3,677 residues
Chains: 11
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hmpv nucleoprotein; RNA
UniProt: Q91F57
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 11 distinct chains · 60% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hmpv nucleoprotein	protein	346	61% helix, 4% strand	Q91F57
B	Hmpv nucleoprotein	protein	367	60% helix, 4% strand	Q91F57
C	Hmpv nucleoprotein	protein	346	61% helix, 4% strand	Q91F57
D	Hmpv nucleoprotein	protein	369	60% helix, 4% strand	Q91F57
E	Hmpv nucleoprotein	protein	364	60% helix, 4% strand	Q91F57
F	Hmpv nucleoprotein	protein	366	60% helix, 4% strand	Q91F57
G	Hmpv nucleoprotein	protein	368	60% helix, 5% strand	Q91F57
H	Hmpv nucleoprotein	protein	351	60% helix, 5% strand	Q91F57
I	Hmpv nucleoprotein	protein	366	60% helix, 5% strand	Q91F57
J	Hmpv nucleoprotein	protein	364	60% helix, 5% strand	Q91F57
K	RNA	rna	70	—	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	846	0.79	0.82	67	empty
2	1043	0.79	0.81	70	empty
3	1140	0.79	0.80	77	empty
4	1174	0.79	0.80	84	empty
5	1001	0.78	0.80	79	empty

Interfaces

26 interfaces between chains.

F–G · 2828 Å² buried · 39 hydrogen bonds · protein-protein
D–E · 2773 Å² buried · 40 hydrogen bonds · protein-protein
A–J · 2708 Å² buried · 36 hydrogen bonds · protein-protein
B–C · 2700 Å² buried · 35 hydrogen bonds · protein-protein
G–H · 2679 Å² buried · 39 hydrogen bonds · protein-protein

Compared structures

5FVC · Structure of RNA-bound decameric HMPV nucleoprotein · the same entry in another collection · chain I against I, 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 Q91F57
Elsewhere: RCSB PDB 5FVC · PDBe 5FVC · UniProt Q91F57

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