SMTL ID : 1nd3.2 (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-5-5-5-5-mer

Ligands

5 x ZN: ZINC ION(Non-covalent)

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

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

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