MolNFT v1 · #15609 · protein

The structure of HRV14 when complexed with pleconaril

1NA1 · Coat protein VP1: “The structure of HRV14 when complexed with pleconaril”. X-ray diffraction, 1 ligand (W11), 11 pockets (best druggability 0.79). MolNFT v1 #15609 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1NA1
Type: protein
Length: 804 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coat protein VP1; Coat protein VP2; Coat protein VP3; Coat protein VP4
UniProt: P03303
Ligands: W11
Pockets: 11 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 12% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Coat protein VP1	protein	273	11% helix, 33% strand	P03303
B	Coat protein VP2	protein	255	15% helix, 37% strand	P03303
C	Coat protein VP3	protein	236	10% helix, 31% strand	P03303
D	Coat protein VP4	protein	40	18% helix, 3% strand	P03303

Ligands and binding sites

W11 · 3-{3,5-dimethyl-4-[3-(3-methyl-isoxazol-5-yl)-propoxy]-phenyl}-5-trifluoromethyl-[1,2,4]oxadiazole · ligand · chains A, C

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

Pockets

11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	270	0.79	0.91	41	W11
2	212	0.51	0.76	36	empty
3	132	0.46	0.78	24	empty
4	133	0.44	0.76	29	empty
5	110	0.38	0.74	23	empty

Interfaces

6 interfaces between chains.

A–C · 4118 Å² buried · 75 hydrogen bonds · protein-protein
A–B · 2124 Å² buried · 43 hydrogen bonds · protein-protein
B–C · 1717 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 957 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 909 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

1NA1 · The structure of HRV14 when complexed with Pleconaril · 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 P03303
Elsewhere: RCSB PDB 1NA1 · PDBe 1NA1 · UniProt P03303

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