SMTL ID : 1ncr.2 (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-5-5-5-5-mer

Ligands

5 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain E: H.134 Chain I: H.134 Ligands: ZN.4, ZN.7, ZN.10, ZN.13 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:H.134 ZN.4: 6 residues within 4Å: Chain I: H.134 Chain M: H.134 Ligands: ZN.1, ZN.7, ZN.10, ZN.13 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:H.134 ZN.7: 6 residues within 4Å: Chain M: H.134 Chain Q: H.134 Ligands: ZN.1, ZN.4, ZN.10, ZN.13 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:H.134 ZN.10: 6 residues within 4Å: Chain A: H.134 Chain Q: H.134 Ligands: ZN.1, ZN.4, ZN.7, ZN.13 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.134 ZN.13: 6 residues within 4Å: Chain A: H.134 Chain E: H.134 Ligands: ZN.1, ZN.4, ZN.7, ZN.10 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:H.134

5 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

5 x MYR: MYRISTIC ACID(Non-covalent)

MYR.3: 11 residues within 4Å: Chain D: G.1, I.29, N.30 Chain E: Y.6 Chain H: Y.26, F.27, I.29 Chain L: F.27 Chain O: L.2 Ligands: MYR.6, MYR.15 5 PLIP interactions: 1 interactions with chain L, 2 interactions with chain H, 1 interactions with chain O, 1 interactions with chain D Hydrophobic interactions: L:F.27, H:F.27, H:I.29, O:L.2, D:I.29 MYR.6: 11 residues within 4Å: Chain H: G.1, I.29, N.30 Chain I: Y.6 Chain L: Y.26, F.27, I.29 Chain P: F.27 Chain S: L.2 Ligands: MYR.3, MYR.9 5 PLIP interactions: 2 interactions with chain L, 1 interactions with chain S, 1 interactions with chain P, 1 interactions with chain H Hydrophobic interactions: L:F.27, L:I.29, S:L.2, P:F.27, H:I.29 MYR.9: 11 residues within 4Å: Chain C: L.2 Chain L: G.1, I.29, N.30 Chain M: Y.6 Chain P: Y.26, F.27, I.29 Chain T: F.27 Ligands: MYR.6, MYR.12 5 PLIP interactions: 2 interactions with chain P, 1 interactions with chain C, 1 interactions with chain L, 1 interactions with chain T Hydrophobic interactions: P:F.27, P:I.29, C:L.2, L:I.29, T:F.27 MYR.12: 11 residues within 4Å: Chain D: F.27 Chain G: L.2 Chain P: G.1, I.29, N.30 Chain Q: Y.6 Chain T: Y.26, F.27, I.29 Ligands: MYR.9, MYR.15 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain T, 1 interactions with chain P, 1 interactions with chain G Hydrophobic interactions: D:F.27, T:F.27, T:I.29, P:I.29, G:L.2 MYR.15: 11 residues within 4Å: Chain A: Y.6 Chain D: Y.26, F.27, I.29 Chain H: F.27 Chain K: L.2 Chain T: G.1, I.29, N.30 Ligands: MYR.3, MYR.12 5 PLIP interactions: 1 interactions with chain H, 2 interactions with chain D, 1 interactions with chain T, 1 interactions with chain K Hydrophobic interactions: H:F.27, D:F.27, D:I.29, T:I.29, K:L.2

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: AEIMQ
coat protein VP2: BFJNR
coat protein VP3: CGKOS
coat protein VP4: DHLPT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

M
A

Q
A

B
B

F
B

J
B

N
B

R
B

C
C

G
C

K
C

O
C

S
C

D
D

H
D

L
D

P
D

T
D

coat protein VP1

coat protein VP2

coat protein VP3

coat protein VP4

Related Entries With Identical Sequence