SMTL ID : 1nd2.2 (3 other biounits)

The structure of Rhinovirus 16

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 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 4 PLIP interactions: 1 interactions with chain M, 1 interactions with chain I, 1 interactions with chain E, 1 interactions with chain A Metal complexes: 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 4 PLIP interactions: 1 interactions with chain M, 1 interactions with chain Q, 1 interactions with chain I, 1 interactions with chain E Metal complexes: M:H.134, Q:H.134, I:H.134, E: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 4 PLIP interactions: 1 interactions with chain M, 1 interactions with chain Q, 1 interactions with chain I, 1 interactions with chain A Metal complexes: M:H.134, Q: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 4 PLIP interactions: 1 interactions with chain M, 1 interactions with chain Q, 1 interactions with chain E, 1 interactions with chain A Metal complexes: M:H.134, Q:H.134, E: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 4 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain I, 1 interactions with chain E, 1 interactions with chain A Metal complexes: Q:H.134, I:H.134, E:H.134, A:H.134

10 x MYR: MYRISTIC ACID(Non-covalent)

MYR.2: 14 residues within 4Å: Chain A: I.77, I.98, N.99, L.100, Q.101, F.118, S.120, I.122, L.181, Y.190, N.212, L.217, H.238, H.260 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.77, A:I.98, A:I.98, A:F.118, A:I.122, A:I.122, A:L.181, A:Y.190, A:Y.190, A:L.217 Hydrogen bonds: A:L.100, A:Q.101, A:N.212 Salt bridges: A:H.260 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 6 PLIP interactions: 2 interactions with chain H, 1 interactions with chain D, 2 interactions with chain L, 1 interactions with chain O Hydrophobic interactions: H:I.29, D:I.29, L:F.27, L:F.27, O:L.2 Hydrogen bonds: H:F.27 MYR.5: 14 residues within 4Å: Chain E: I.77, I.98, N.99, L.100, Q.101, F.118, S.120, I.122, L.181, Y.190, N.212, L.217, H.238, H.260 14 PLIP interactions: 14 interactions with chain E Hydrophobic interactions: E:I.77, E:I.98, E:I.98, E:F.118, E:I.122, E:I.122, E:L.181, E:Y.190, E:Y.190, E:L.217 Hydrogen bonds: E:L.100, E:Q.101, E:N.212 Salt bridges: E:H.260 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 6 PLIP interactions: 1 interactions with chain S, 1 interactions with chain H, 2 interactions with chain P, 2 interactions with chain L Hydrophobic interactions: S:L.2, H:I.29, P:F.27, P:F.27, L:I.29 Hydrogen bonds: L:F.27 MYR.8: 14 residues within 4Å: Chain I: I.77, I.98, N.99, L.100, Q.101, F.118, S.120, I.122, L.181, Y.190, N.212, L.217, H.238, H.260 14 PLIP interactions: 14 interactions with chain I Hydrophobic interactions: I:I.77, I:I.98, I:I.98, I:F.118, I:I.122, I:I.122, I:L.181, I:Y.190, I:Y.190, I:L.217 Hydrogen bonds: I:L.100, I:Q.101, I:N.212 Salt bridges: I:H.260 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 6 PLIP interactions: 2 interactions with chain P, 2 interactions with chain T, 1 interactions with chain L, 1 interactions with chain C Hydrophobic interactions: P:I.29, T:F.27, T:F.27, L:I.29, C:L.2 Hydrogen bonds: P:F.27 MYR.11: 14 residues within 4Å: Chain M: I.77, I.98, N.99, L.100, Q.101, F.118, S.120, I.122, L.181, Y.190, N.212, L.217, H.238, H.260 14 PLIP interactions: 14 interactions with chain M Hydrophobic interactions: M:I.77, M:I.98, M:I.98, M:F.118, M:I.122, M:I.122, M:L.181, M:Y.190, M:Y.190, M:L.217 Hydrogen bonds: M:L.100, M:Q.101, M:N.212 Salt bridges: M:H.260 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 6 PLIP interactions: 1 interactions with chain G, 2 interactions with chain T, 1 interactions with chain P, 2 interactions with chain D Hydrophobic interactions: G:L.2, T:I.29, P:I.29, D:F.27, D:F.27 Hydrogen bonds: T:F.27 MYR.14: 14 residues within 4Å: Chain Q: I.77, I.98, N.99, L.100, Q.101, F.118, S.120, I.122, L.181, Y.190, N.212, L.217, H.238, H.260 14 PLIP interactions: 14 interactions with chain Q Hydrophobic interactions: Q:I.77, Q:I.98, Q:I.98, Q:F.118, Q:I.122, Q:I.122, Q:L.181, Q:Y.190, Q:Y.190, Q:L.217 Hydrogen bonds: Q:L.100, Q:Q.101, Q:N.212 Salt bridges: Q:H.260 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 6 PLIP interactions: 2 interactions with chain D, 2 interactions with chain H, 1 interactions with chain K, 1 interactions with chain T Hydrophobic interactions: D:I.29, H:F.27, H:F.27, K:L.2, T:I.29 Hydrogen bonds: D:F.27

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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