SMTL ID : 1nd3.3 (3 other biounits)

The structure of HRV16, when complexed with pleconaril, an antiviral compound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-6-6-6-6-mer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.134 Chain E: H.134 Ligands: ZN.3 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Metal complexes: E:H.134, A:H.134 ZN.3: 3 residues within 4Å: Chain A: H.134 Chain E: H.134 Ligands: ZN.1 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:H.134 ZN.5: 3 residues within 4Å: Chain I: H.134 Chain M: H.134 Ligands: ZN.7 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:H.134 ZN.7: 3 residues within 4Å: Chain I: H.134 Chain M: H.134 Ligands: ZN.5 2 PLIP interactions: 1 interactions with chain M, 1 interactions with chain I Metal complexes: M:H.134, I:H.134 ZN.9: 3 residues within 4Å: Chain Q: H.134 Chain U: H.134 Ligands: ZN.11 2 PLIP interactions: 1 interactions with chain U, 1 interactions with chain Q Metal complexes: U:H.134, Q:H.134 ZN.11: 3 residues within 4Å: Chain Q: H.134 Chain U: H.134 Ligands: ZN.9 1 PLIP interactions: 1 interactions with chain U Metal complexes: U:H.134

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: 16 residues within 4Å: Chain A: I.98, 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 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.98, A:I.122, A:Y.144, A:Y.144, A:L.181, A:L.184, A:Y.190 pi-Stacking: A:Y.190 Halogen bonds: A:A.166 W11.4: 16 residues within 4Å: Chain E: I.98, 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 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:I.98, E:I.122, E:Y.144, E:Y.144, E:L.181, E:L.184, E:Y.190 pi-Stacking: E:Y.190 Halogen bonds: E:A.166 W11.6: 16 residues within 4Å: Chain I: I.98, 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 9 PLIP interactions: 9 interactions with chain I Hydrophobic interactions: I:I.98, I:I.122, I:Y.144, I:Y.144, I:L.181, I:L.184, I:Y.190 pi-Stacking: I:Y.190 Halogen bonds: I:A.166 W11.8: 16 residues within 4Å: Chain M: I.98, 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 9 PLIP interactions: 9 interactions with chain M Hydrophobic interactions: M:I.98, M:I.122, M:Y.144, M:Y.144, M:L.181, M:L.184, M:Y.190 pi-Stacking: M:Y.190 Halogen bonds: M:A.166 W11.10: 16 residues within 4Å: Chain Q: I.98, 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 9 PLIP interactions: 9 interactions with chain Q Hydrophobic interactions: Q:I.98, Q:I.122, Q:Y.144, Q:Y.144, Q:L.181, Q:L.184, Q:Y.190 pi-Stacking: Q:Y.190 Halogen bonds: Q:A.166 W11.12: 16 residues within 4Å: Chain U: I.98, 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 9 PLIP interactions: 9 interactions with chain U Hydrophobic interactions: U:I.98, U:I.122, U:Y.144, U:Y.144, U:L.181, U:L.184, U:Y.190 pi-Stacking: U:Y.190 Halogen bonds: U:A.166

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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