SMTL ID : 3j9f.3 (3 other biounits)

Poliovirus complexed with soluble, deglycosylated poliovirus receptor (Pvr) at 4 degrees C

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

12 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG-NAG-BMA.1: 5 residues within 4Å: Chain E: Y.23, V.68, A.69, N.78, S.80 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 5 residues within 4Å: Chain F: G.75, K.76, N.77, N.96 Ligands: NAG-NAG.4 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 5 residues within 4Å: Chain L: Y.23, V.68, A.69, N.78, S.80 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 5 residues within 4Å: Chain M: G.75, K.76, N.77, N.96 Ligands: NAG-NAG.12 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 5 residues within 4Å: Chain S: Y.23, V.68, A.69, N.78, S.80 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 5 residues within 4Å: Chain T: G.75, K.76, N.77, N.96 Ligands: NAG-NAG.20 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.25: 5 residues within 4Å: Chain Z: Y.23, V.68, A.69, N.78, S.80 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.29: 5 residues within 4Å: Chain 0: G.75, K.76, N.77, N.96 Ligands: NAG-NAG.28 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.33: 5 residues within 4Å: Chain 6: Y.23, V.68, A.69, N.78, S.80 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.37: 5 residues within 4Å: Chain 7: G.75, K.76, N.77, N.96 Ligands: NAG-NAG.36 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.41: 5 residues within 4Å: Chain d: Y.23, V.68, A.69, N.78, S.80 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.45: 5 residues within 4Å: Ligands: NAG-NAG.44 Chain e: G.75, K.76, N.77, N.96 No protein-ligand interaction detected (PLIP)

6 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-FUC.2: 4 residues within 4Å: Chain E: E.91, G.92, N.93, W.111 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-FUC.10: 4 residues within 4Å: Chain L: E.91, G.92, N.93, W.111 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-FUC.18: 4 residues within 4Å: Chain S: E.91, G.92, N.93, W.111 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-FUC.26: 4 residues within 4Å: Chain Z: E.91, G.92, N.93, W.111 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-FUC.34: 4 residues within 4Å: Chain 6: E.91, G.92, N.93, W.111 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-FUC.42: 4 residues within 4Å: Chain d: E.91, G.92, N.93, W.111 No protein-ligand interaction detected (PLIP)

12 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 1 residues within 4Å: Chain F: N.47 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain F: N.77, T.94 Ligands: NAG-NAG-BMA.5 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain M: N.47 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain M: N.77, T.94 Ligands: NAG-NAG-BMA.13 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 1 residues within 4Å: Chain T: N.47 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain T: N.77, T.94 Ligands: NAG-NAG-BMA.21 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 1 residues within 4Å: Chain 0: N.47 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 3 residues within 4Å: Chain 0: N.77, T.94 Ligands: NAG-NAG-BMA.29 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 1 residues within 4Å: Chain 7: N.47 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 3 residues within 4Å: Chain 7: N.77, T.94 Ligands: NAG-NAG-BMA.37 No protein-ligand interaction detected (PLIP) NAG-NAG.43: 1 residues within 4Å: Chain e: N.47 No protein-ligand interaction detected (PLIP) NAG-NAG.44: 3 residues within 4Å: Ligands: NAG-NAG-BMA.45 Chain e: N.77, T.94 No protein-ligand interaction detected (PLIP)

6 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.6: 2 residues within 4Å: Chain G: P.64, N.66 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.14: 2 residues within 4Å: Chain N: P.64, N.66 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.22: 2 residues within 4Å: Chain U: P.64, N.66 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.30: 2 residues within 4Å: Chain 1: P.64, N.66 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.38: 2 residues within 4Å: Chain 8: P.64, N.66 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.46: 2 residues within 4Å: Chain f: P.64, N.66 No protein-ligand interaction detected (PLIP)

6 x PLM: PALMITIC ACID(Non-covalent)

PLM.7: 15 residues within 4Å: Chain A: I.110, Y.112, F.130, M.132, L.134, Y.159, P.181, I.183, I.194, V.196, V.199, Y.205, S.206, N.235, F.237 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.110, A:Y.112, A:F.130, A:L.134, A:Y.159, A:Y.159, A:Y.159, A:I.183, A:V.196, A:V.199, A:Y.205, A:F.237, A:F.237 Hydrogen bonds: A:Y.112 PLM.15: 15 residues within 4Å: Chain H: I.110, Y.112, F.130, M.132, L.134, Y.159, P.181, I.183, I.194, V.196, V.199, Y.205, S.206, N.235, F.237 14 PLIP interactions: 14 interactions with chain H Hydrophobic interactions: H:I.110, H:Y.112, H:F.130, H:L.134, H:Y.159, H:Y.159, H:Y.159, H:I.183, H:V.196, H:V.199, H:Y.205, H:F.237, H:F.237 Hydrogen bonds: H:Y.112 PLM.23: 15 residues within 4Å: Chain O: I.110, Y.112, F.130, M.132, L.134, Y.159, P.181, I.183, I.194, V.196, V.199, Y.205, S.206, N.235, F.237 14 PLIP interactions: 14 interactions with chain O Hydrophobic interactions: O:I.110, O:Y.112, O:F.130, O:L.134, O:Y.159, O:Y.159, O:Y.159, O:I.183, O:V.196, O:V.199, O:Y.205, O:F.237, O:F.237 Hydrogen bonds: O:Y.112 PLM.31: 15 residues within 4Å: Chain V: I.110, Y.112, F.130, M.132, L.134, Y.159, P.181, I.183, I.194, V.196, V.199, Y.205, S.206, N.235, F.237 14 PLIP interactions: 14 interactions with chain V Hydrophobic interactions: V:I.110, V:Y.112, V:F.130, V:L.134, V:Y.159, V:Y.159, V:Y.159, V:I.183, V:V.196, V:V.199, V:Y.205, V:F.237, V:F.237 Hydrogen bonds: V:Y.112 PLM.39: 15 residues within 4Å: Chain 2: I.110, Y.112, F.130, M.132, L.134, Y.159, P.181, I.183, I.194, V.196, V.199, Y.205, S.206, N.235, F.237 14 PLIP interactions: 14 interactions with chain 2 Hydrophobic interactions: 2:I.110, 2:Y.112, 2:F.130, 2:L.134, 2:Y.159, 2:Y.159, 2:Y.159, 2:I.183, 2:V.196, 2:V.199, 2:Y.205, 2:F.237, 2:F.237 Hydrogen bonds: 2:Y.112 PLM.47: 15 residues within 4Å: Chain 9: I.110, Y.112, F.130, M.132, L.134, Y.159, P.181, I.183, I.194, V.196, V.199, Y.205, S.206, N.235, F.237 14 PLIP interactions: 14 interactions with chain 9 Hydrophobic interactions: 9:I.110, 9:Y.112, 9:F.130, 9:L.134, 9:Y.159, 9:Y.159, 9:Y.159, 9:I.183, 9:V.196, 9:V.199, 9:Y.205, 9:F.237, 9:F.237 Hydrogen bonds: 9:Y.112

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.8: 3 residues within 4Å: Chain G: N.72, T.74, Q.81 No protein-ligand interaction detected (PLIP) NAG.16: 3 residues within 4Å: Chain N: N.72, T.74, Q.81 No protein-ligand interaction detected (PLIP) NAG.24: 3 residues within 4Å: Chain U: N.72, T.74, Q.81 No protein-ligand interaction detected (PLIP) NAG.32: 3 residues within 4Å: Chain 1: N.72, T.74, Q.81 No protein-ligand interaction detected (PLIP) NAG.40: 3 residues within 4Å: Chain 8: N.72, T.74, Q.81 1 PLIP interactions: 1 interactions with chain 8 Hydrogen bonds: 8:T.74 NAG.48: 3 residues within 4Å: Chain f: N.72, T.74, Q.81 1 PLIP interactions: 1 interactions with chain f Hydrogen bonds: f:T.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Strauss, M. et al., Nectin-Like Interactions between Poliovirus and Its Receptor Trigger Conformational Changes Associated with Cell Entry. J.Virol. (2015)

Release Date

2015-02-11

Peptides

Protein VP1: AHOV29
Protein VP2: BIPW3a
Protein VP3: CJQX4b
Protein VP4: DKRY5c
Poliovirus receptor: ELSZ6d
Poliovirus receptor: FMT07e
Poliovirus receptor: GNU18f

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

H
1

O
1

V
1

2
1

9
1

B
2

I
2

P
2

W
2

3
2

a
2

C
3

J
3

Q
3

X
3

4
3

b
3

D
4

K
4

R
4

Y
4

5
4

c
4

E
7

L
7

S
7

Z
7

6
7

d
7

F
8

M
8

T
8

0
8

7
8

e
8

G
9

N
9

U
9

1
9

8
9

f
9

Protein VP1

Protein VP2

Protein VP3

Protein VP4

Poliovirus receptor

Poliovirus receptor

Poliovirus receptor

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