SMTL ID : 1qjy.2 (3 other biounits)

HUMAN RHINOVIRUS 16 COAT PROTEIN IN COMPLEX WITH ANTIVIRAL COMPOUND VP65099

Coordinates

PDB Format Compare

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.4, ZN.7, ZN.10, ZN.13 5 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain M, 1 interactions with chain I, 1 interactions with chain E, 1 interactions with chain A Metal complexes: Q:H.134, M:H.134, I:H.134, E:H.134, A:H.134 ZN.4: 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.7, ZN.10, ZN.13 5 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain M, 1 interactions with chain E, 1 interactions with chain I, 1 interactions with chain A Metal complexes: Q:H.134, M:H.134, E:H.134, I: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.4, ZN.10, ZN.13 5 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain M, 1 interactions with chain E, 1 interactions with chain I, 1 interactions with chain A Metal complexes: Q:H.134, M:H.134, E:H.134, I:H.134, A:H.134 ZN.10: 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.4, ZN.7, ZN.13 5 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain M, 1 interactions with chain E, 1 interactions with chain I, 1 interactions with chain A Metal complexes: Q:H.134, M:H.134, E:H.134, I:H.134, A:H.134 ZN.13: 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.4, ZN.7, ZN.10 5 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain M, 1 interactions with chain E, 1 interactions with chain I, 1 interactions with chain A Metal complexes: Q:H.134, M:H.134, E:H.134, I:H.134, A:H.134

5 x W03: 2,6-DIMETHYL-1-(3-[3-METHYL-5-ISOXAZOLYL]-PROPANYL)-4-[2-METHYL-4-ISOXAZOLYL]-PHENOL(Non-covalent)

W03.2: 14 residues within 4Å: Chain A: I.98, L.100, I.122, Y.142, Y.144, A.166, V.168, F.179, L.181, L.184, Y.190, M.214, L.217, I.236 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.98, A:I.122, A:Y.142, A:Y.144, A:Y.144, A:V.168, A:F.179, A:F.179, A:L.181, A:L.184, A:Y.190, A:Y.190, A:I.236 Water bridges: A:L.100 W03.5: 14 residues within 4Å: Chain E: I.98, L.100, I.122, Y.142, Y.144, A.166, V.168, F.179, L.181, L.184, Y.190, M.214, L.217, I.236 14 PLIP interactions: 14 interactions with chain E Hydrophobic interactions: E:I.98, E:I.122, E:Y.142, E:Y.144, E:Y.144, E:V.168, E:F.179, E:F.179, E:L.181, E:L.184, E:Y.190, E:Y.190, E:I.236 Water bridges: E:L.100 W03.8: 14 residues within 4Å: Chain I: I.98, L.100, I.122, Y.142, Y.144, A.166, V.168, F.179, L.181, L.184, Y.190, M.214, L.217, I.236 14 PLIP interactions: 14 interactions with chain I Hydrophobic interactions: I:I.98, I:I.122, I:Y.142, I:Y.144, I:Y.144, I:V.168, I:F.179, I:F.179, I:L.181, I:L.184, I:Y.190, I:Y.190, I:I.236 Water bridges: I:L.100 W03.11: 14 residues within 4Å: Chain M: I.98, L.100, I.122, Y.142, Y.144, A.166, V.168, F.179, L.181, L.184, Y.190, M.214, L.217, I.236 14 PLIP interactions: 14 interactions with chain M Hydrophobic interactions: M:I.98, M:I.122, M:Y.142, M:Y.144, M:Y.144, M:V.168, M:F.179, M:F.179, M:L.181, M:L.184, M:Y.190, M:Y.190, M:I.236 Water bridges: M:L.100 W03.14: 14 residues within 4Å: Chain Q: I.98, L.100, I.122, Y.142, Y.144, A.166, V.168, F.179, L.181, L.184, Y.190, M.214, L.217, I.236 14 PLIP interactions: 14 interactions with chain Q Hydrophobic interactions: Q:I.98, Q:I.122, Q:Y.142, Q:Y.144, Q:Y.144, Q:V.168, Q:F.179, Q:F.179, Q:L.181, Q:L.184, Q:Y.190, Q:Y.190, Q:I.236 Water bridges: Q:L.100

5 x MYR: MYRISTIC ACID(Covalent)

MYR.3: 11 residues within 4Å: Chain D: G.1, N.30 Chain E: Y.6 Chain H: Y.26, F.27, I.29, Y.31 Chain L: F.27 Chain O: L.2 Ligands: MYR.6, MYR.15 4 PLIP interactions: 1 interactions with chain E, 1 interactions with chain H, 1 interactions with chain O, 1 interactions with chain L Hydrogen bonds: E:Y.6 Hydrophobic interactions: H:Y.26, O:L.2, L:F.27 MYR.6: 11 residues within 4Å: Chain H: G.1, N.30 Chain I: Y.6 Chain L: Y.26, F.27, I.29, Y.31 Chain P: F.27 Chain S: L.2 Ligands: MYR.3, MYR.9 3 PLIP interactions: 1 interactions with chain P, 1 interactions with chain L, 1 interactions with chain S Hydrophobic interactions: P:F.27, L:Y.26, S:L.2 MYR.9: 11 residues within 4Å: Chain C: L.2 Chain L: G.1, N.30 Chain M: Y.6 Chain P: Y.26, F.27, I.29, Y.31 Chain T: F.27 Ligands: MYR.6, MYR.12 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain T, 1 interactions with chain P Hydrophobic interactions: C:L.2, T:F.27, P:Y.26 MYR.12: 11 residues within 4Å: Chain D: F.27 Chain G: L.2 Chain P: G.1, N.30 Chain Q: Y.6 Chain T: Y.26, F.27, I.29, Y.31 Ligands: MYR.9, MYR.15 3 PLIP interactions: 1 interactions with chain G, 1 interactions with chain T, 1 interactions with chain D Hydrophobic interactions: G:L.2, T:Y.26, D:F.27 MYR.15: 11 residues within 4Å: Chain A: Y.6 Chain D: Y.26, F.27, I.29, Y.31 Chain H: F.27 Chain K: L.2 Chain T: G.1, N.30 Ligands: MYR.3, MYR.12 4 PLIP interactions: 1 interactions with chain H, 1 interactions with chain A, 1 interactions with chain D, 1 interactions with chain K Hydrophobic interactions: H:F.27, D:Y.26, K:L.2 Hydrogen bonds: A:Y.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hadfield, A.T. et al., Analysis of Three Structurally Related Antiviral Compounds in Complex with Human Rhinovirus 16. Proc.Natl.Acad.Sci.USA (1999)

Release Date

1999-07-20

Peptides

PROTEIN VP1: AEIMQ
PROTEIN VP2: BFJNR
PROTEIN VP3: CGKOS
PROTEIN VP4: DHLPT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

E
1

I
1

M
1

Q
1

B
2

F
2

J
2

N
2

R
2

C
3

G
3

K
3

O
3

S
3

D
4

H
4

L
4

P
4

T
4

PROTEIN VP1

PROTEIN VP2

PROTEIN VP3

PROTEIN VP4

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