SMTL ID : 1ncr.3 (3 other biounits)

The structure of Rhinovirus 16 when complexed with pleconaril, an antiviral compound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-6-6-6-6-mer

Ligands

6 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.1: 2 residues within 4Å: Chain E: H.134 Ligands: ZN.4 No protein-ligand interaction detected (PLIP) ZN.4: 1 residues within 4Å: Ligands: ZN.1 No protein-ligand interaction detected (PLIP) ZN.7: 1 residues within 4Å: Ligands: ZN.10 No protein-ligand interaction detected (PLIP) ZN.10: 2 residues within 4Å: Chain I: H.134 Ligands: ZN.7 No protein-ligand interaction detected (PLIP) ZN.13: 2 residues within 4Å: Chain U: H.134 Ligands: ZN.16 No protein-ligand interaction detected (PLIP) ZN.16: 1 residues within 4Å: Ligands: ZN.13 No protein-ligand interaction detected (PLIP)

6 x W11: 3-{3,5-DIMETHYL-4-[3-(3-METHYL-ISOXAZOL-5-YL)-PROPOXY]-PHENYL}-5-TRIFLUOROMETHYL-[1,2,4]OXADIAZOLE(Non-covalent)

W11.2: 17 residues within 4Å: Chain A: I.98, L.100, I.122, M.124, Y.142, M.143, Y.144, A.166, S.167, V.168, F.179, L.181, L.184, Y.190, N.212, M.214, L.217 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.98, A:L.100, A:I.122, A:Y.144, A:Y.144, A:L.181, A:L.184, A:Y.190 Water bridges: A:L.100 pi-Stacking: A:Y.190 Halogen bonds: A:A.166 W11.5: 17 residues within 4Å: Chain E: I.98, L.100, I.122, M.124, Y.142, M.143, Y.144, A.166, S.167, V.168, F.179, L.181, L.184, Y.190, N.212, M.214, L.217 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:I.98, E:L.100, E:I.122, E:Y.144, E:Y.144, E:L.181, E:L.184, E:Y.190 Water bridges: E:L.100 pi-Stacking: E:Y.190 Halogen bonds: E:A.166 W11.8: 17 residues within 4Å: Chain I: I.98, L.100, I.122, M.124, Y.142, M.143, Y.144, A.166, S.167, V.168, F.179, L.181, L.184, Y.190, N.212, M.214, L.217 11 PLIP interactions: 11 interactions with chain I Hydrophobic interactions: I:I.98, I:L.100, I:I.122, I:Y.144, I:Y.144, I:L.181, I:L.184, I:Y.190 Water bridges: I:L.100 pi-Stacking: I:Y.190 Halogen bonds: I:A.166 W11.11: 17 residues within 4Å: Chain M: I.98, L.100, I.122, M.124, Y.142, M.143, Y.144, A.166, S.167, V.168, F.179, L.181, L.184, Y.190, N.212, M.214, L.217 11 PLIP interactions: 11 interactions with chain M Hydrophobic interactions: M:I.98, M:L.100, M:I.122, M:Y.144, M:Y.144, M:L.181, M:L.184, M:Y.190 Water bridges: M:L.100 pi-Stacking: M:Y.190 Halogen bonds: M:A.166 W11.14: 17 residues within 4Å: Chain Q: I.98, L.100, I.122, M.124, Y.142, M.143, Y.144, A.166, S.167, V.168, F.179, L.181, L.184, Y.190, N.212, M.214, L.217 11 PLIP interactions: 11 interactions with chain Q Hydrophobic interactions: Q:I.98, Q:L.100, Q:I.122, Q:Y.144, Q:Y.144, Q:L.181, Q:L.184, Q:Y.190 Water bridges: Q:L.100 pi-Stacking: Q:Y.190 Halogen bonds: Q:A.166 W11.17: 17 residues within 4Å: Chain U: I.98, L.100, I.122, M.124, Y.142, M.143, Y.144, A.166, S.167, V.168, F.179, L.181, L.184, Y.190, N.212, M.214, L.217 11 PLIP interactions: 11 interactions with chain U Hydrophobic interactions: U:I.98, U:L.100, U:I.122, U:Y.144, U:Y.144, U:L.181, U:L.184, U:Y.190 Water bridges: U:L.100 pi-Stacking: U:Y.190 Halogen bonds: U:A.166

6 x MYR: MYRISTIC ACID(Non-covalent)

MYR.3: 8 residues within 4Å: Chain D: G.1, I.29, N.30 Chain E: Y.6 Chain H: Y.26, F.27, I.29 Ligands: MYR.6 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain H Hydrophobic interactions: D:I.29, H:F.27, H:I.29 MYR.6: 4 residues within 4Å: Chain H: G.1, I.29, N.30 Ligands: MYR.3 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:I.29 MYR.9: 4 residues within 4Å: Chain L: G.1, I.29, N.30 Ligands: MYR.12 1 PLIP interactions: 1 interactions with chain L Hydrophobic interactions: L:I.29 MYR.12: 8 residues within 4Å: Chain I: Y.6 Chain L: Y.26, F.27, I.29 Chain P: G.1, I.29, N.30 Ligands: MYR.9 4 PLIP interactions: 2 interactions with chain L, 1 interactions with chain P, 1 interactions with chain I Hydrophobic interactions: L:F.27, L:I.29, P:I.29 Hydrogen bonds: I:Y.6 MYR.15: 8 residues within 4Å: Chain T: G.1, I.29, N.30 Chain U: Y.6 Chain X: Y.26, F.27, I.29 Ligands: MYR.18 3 PLIP interactions: 2 interactions with chain X, 1 interactions with chain T Hydrophobic interactions: X:F.27, X:I.29, T:I.29 MYR.18: 4 residues within 4Å: Chain X: G.1, I.29, N.30 Ligands: MYR.15 1 PLIP interactions: 1 interactions with chain X Hydrophobic interactions: X:I.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y. et al., Structural and virological studies of the stages of virus replication that are affected by antirhinovirus compounds. J.Virol. (2004)

Release Date

2003-12-16

Peptides

coat protein VP1: AEIMQU
coat protein VP2: BFJNRV
coat protein VP3: CGKOSW
coat protein VP4: DHLPTX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

M
A

Q
A

U
A

B
B

F
B

J
B

N
B

R
B

V
B

C
C

G
C

K
C

O
C

S
C

W
C

D
D

H
D

L
D

P
D

T
D

X
D

coat protein VP1

coat protein VP2

coat protein VP3

coat protein VP4

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