SMTL ID : 3epd.3 (3 other biounits)

CryoEM structure of poliovirus receptor bound to poliovirus type 3

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-6-6-6-mer

Ligands

6 x ILE- SER- GLU- VAL: Poliovirus Type3 peptide(Non-covalent)

ILE-SER-GLU-VAL.1: 5 residues within 4Å: Chain D: A.2, Q.3, V.4, S.5, N.25 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:A.2, D:V.4 Hydrogen bonds: D:A.2, D:Q.3, D:V.4, D:V.4, D:S.6, D:N.25 ILE-SER-GLU-VAL.4: 6 residues within 4Å: Chain I: A.2, Q.3, V.4, S.5, N.25 Ligands: MYR.3 8 PLIP interactions: 8 interactions with chain I Hydrophobic interactions: I:A.2, I:V.4 Hydrogen bonds: I:A.2, I:Q.3, I:V.4, I:V.4, I:S.6, I:N.25 ILE-SER-GLU-VAL.7: 6 residues within 4Å: Chain N: A.2, Q.3, V.4, S.5, N.25 Ligands: MYR.12 9 PLIP interactions: 9 interactions with chain N Hydrophobic interactions: N:A.2, N:V.4 Hydrogen bonds: N:A.2, N:Q.3, N:V.4, N:V.4, N:S.6, N:N.25, N:N.25 ILE-SER-GLU-VAL.10: 5 residues within 4Å: Chain S: A.2, Q.3, V.4, S.5, N.25 8 PLIP interactions: 8 interactions with chain S Hydrophobic interactions: S:A.2, S:V.4 Hydrogen bonds: S:A.2, S:Q.3, S:V.4, S:V.4, S:S.6, S:N.25 ILE-SER-GLU-VAL.13: 5 residues within 4Å: Chain X: A.2, Q.3, V.4, S.5, N.25 9 PLIP interactions: 9 interactions with chain X Hydrophobic interactions: X:A.2, X:V.4 Hydrogen bonds: X:A.2, X:Q.3, X:V.4, X:V.4, X:S.6, X:N.25, X:N.25 ILE-SER-GLU-VAL.16: 6 residues within 4Å: Chain 2: A.2, Q.3, V.4, S.5, N.25 Ligands: MYR.15 8 PLIP interactions: 8 interactions with chain 2 Hydrophobic interactions: 2:A.2, 2:V.4 Hydrogen bonds: 2:A.2, 2:Q.3, 2:V.4, 2:V.4, 2:S.6, 2:N.25

6 x SPH: SPHINGOSINE(Non-covalent)

SPH.2: 13 residues within 4Å: Chain B: I.87, Y.89, F.107, F.111, Y.136, I.160, I.171, V.173, Y.182, S.183, H.184, M.210, F.215 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:I.87, B:Y.89, B:F.107, B:F.111, B:Y.136, B:Y.136, B:I.160, B:I.171, B:V.173, B:Y.182, B:F.215, B:F.215, B:F.215 Hydrogen bonds: B:S.183, B:S.183 SPH.5: 13 residues within 4Å: Chain G: I.87, Y.89, F.107, F.111, Y.136, I.160, I.171, V.173, Y.182, S.183, H.184, M.210, F.215 16 PLIP interactions: 16 interactions with chain G Hydrophobic interactions: G:I.87, G:Y.89, G:F.107, G:F.111, G:Y.136, G:Y.136, G:I.160, G:I.171, G:V.173, G:Y.182, G:F.215, G:F.215, G:F.215 Hydrogen bonds: G:Y.89, G:S.183, G:S.183 SPH.8: 13 residues within 4Å: Chain L: I.87, Y.89, F.107, F.111, Y.136, I.160, I.171, V.173, Y.182, S.183, H.184, M.210, F.215 16 PLIP interactions: 16 interactions with chain L Hydrophobic interactions: L:I.87, L:Y.89, L:F.107, L:F.111, L:Y.136, L:Y.136, L:I.160, L:I.171, L:V.173, L:Y.182, L:F.215, L:F.215, L:F.215 Hydrogen bonds: L:Y.89, L:S.183, L:S.183 SPH.11: 13 residues within 4Å: Chain Q: I.87, Y.89, F.107, F.111, Y.136, I.160, I.171, V.173, Y.182, S.183, H.184, M.210, F.215 16 PLIP interactions: 16 interactions with chain Q Hydrophobic interactions: Q:I.87, Q:Y.89, Q:F.107, Q:F.111, Q:Y.136, Q:Y.136, Q:I.160, Q:I.171, Q:V.173, Q:Y.182, Q:F.215, Q:F.215, Q:F.215 Hydrogen bonds: Q:Y.89, Q:S.183, Q:S.183 SPH.14: 13 residues within 4Å: Chain V: I.87, Y.89, F.107, F.111, Y.136, I.160, I.171, V.173, Y.182, S.183, H.184, M.210, F.215 15 PLIP interactions: 15 interactions with chain V Hydrophobic interactions: V:I.87, V:Y.89, V:F.107, V:F.111, V:Y.136, V:Y.136, V:I.160, V:I.171, V:V.173, V:Y.182, V:F.215, V:F.215, V:F.215 Hydrogen bonds: V:S.183, V:S.183 SPH.17: 13 residues within 4Å: Chain 0: I.87, Y.89, F.107, F.111, Y.136, I.160, I.171, V.173, Y.182, S.183, H.184, M.210, F.215 16 PLIP interactions: 16 interactions with chain 0 Hydrophobic interactions: 0:I.87, 0:Y.89, 0:F.107, 0:F.111, 0:Y.136, 0:Y.136, 0:I.160, 0:I.171, 0:V.173, 0:Y.182, 0:F.215, 0:F.215, 0:F.215 Hydrogen bonds: 0:Y.89, 0:S.183, 0:S.183

6 x MYR: MYRISTIC ACID(Covalent)

MYR.3: 11 residues within 4Å: Chain D: G.1, A.2, I.29, Y.31 Chain I: A.2, V.4, T.27, T.28, I.29, Y.31 Ligands: ILE-SER-GLU-VAL.4 4 PLIP interactions: 2 interactions with chain I, 2 interactions with chain D Hydrophobic interactions: I:A.2, D:I.29, D:Y.31 Hydrogen bonds: I:T.27 MYR.6: 4 residues within 4Å: Chain I: G.1, A.2, I.29, Y.31 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:I.29, I:Y.31 MYR.9: 4 residues within 4Å: Chain N: G.1, A.2, I.29, Y.31 2 PLIP interactions: 2 interactions with chain N Hydrophobic interactions: N:I.29, N:Y.31 MYR.12: 11 residues within 4Å: Chain N: A.2, V.4, T.27, T.28, I.29, Y.31 Chain S: G.1, A.2, I.29, Y.31 Ligands: ILE-SER-GLU-VAL.7 4 PLIP interactions: 2 interactions with chain S, 2 interactions with chain N Hydrophobic interactions: S:I.29, S:Y.31, N:A.2 Hydrogen bonds: N:T.27 MYR.15: 11 residues within 4Å: Chain 2: A.2, V.4, T.27, T.28, I.29, Y.31 Chain X: G.1, A.2, I.29, Y.31 Ligands: ILE-SER-GLU-VAL.16 4 PLIP interactions: 2 interactions with chain X, 2 interactions with chain 2 Hydrophobic interactions: X:I.29, X:Y.31, 2:A.2 Hydrogen bonds: 2:T.27 MYR.18: 4 residues within 4Å: Chain 2: G.1, A.2, I.29, Y.31 2 PLIP interactions: 2 interactions with chain 2 Hydrophobic interactions: 2:I.29, 2:Y.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, P. et al., Crystal structure of CD155 and electron microscopic studies of its complexes with polioviruses. Proc.Natl.Acad.Sci.USA (2008)

Release Date

2008-11-11

Peptides

Poliovirus receptor: AFKPUZ
protein VP1: BGLQV0
protein VP2: CHMRW1
protein VP4: DINSX2
protein VP3: EJOTY3

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
R

F
R

K
R

P
R

U
R

Z
R

B
1

G
1

L
1

Q
1

V
1

0
1

C
2

H
2

M
2

R
2

W
2

1
2

D
4

I
4

N
4

S
4

X
4

2
4

E
3

J
3

O
3

T
3

Y
3

3
3

Poliovirus receptor

protein VP1

protein VP2

protein VP4

protein VP3

Related Entries With Identical Sequence