SMTL ID : 6i2k.2 (3 other biounits)

Structure of EV71 complexed with its receptor SCARB2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-5-5-5-5-5-mer

Ligands

5 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 7 residues within 4Å: Chain E: N.44, V.45, V.62, L.108, I.109, R.110, T.146 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.10: 7 residues within 4Å: Chain J: N.44, V.45, V.62, L.108, I.109, R.110, T.146 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.19: 7 residues within 4Å: Chain O: N.44, V.45, V.62, L.108, I.109, R.110, T.146 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.28: 7 residues within 4Å: Chain T: N.44, V.45, V.62, L.108, I.109, R.110, T.146 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.37: 7 residues within 4Å: Chain Y: N.44, V.45, V.62, L.108, I.109, R.110, T.146 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 5 residues within 4Å: Chain E: L.70, Y.93, V.94, W.154, N.182 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain E: N.280 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain J: L.70, Y.93, V.94, W.154, N.182 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain J: N.280 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 5 residues within 4Å: Chain O: L.70, Y.93, V.94, W.154, N.182 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 1 residues within 4Å: Chain O: N.280 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 5 residues within 4Å: Chain T: L.70, Y.93, V.94, W.154, N.182 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 1 residues within 4Å: Chain T: N.280 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 5 residues within 4Å: Chain Y: L.70, Y.93, V.94, W.154, N.182 No protein-ligand interaction detected (PLIP) NAG-NAG.40: 1 residues within 4Å: Chain Y: N.280 No protein-ligand interaction detected (PLIP)

5 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

NAG-NAG-BMA.3: 7 residues within 4Å: Chain E: K.220, M.223, N.225, Y.243, R.251, S.252, D.283 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.220, E:D.283 NAG-NAG-BMA.12: 7 residues within 4Å: Chain J: K.220, M.223, N.225, Y.243, R.251, S.252, D.283 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:K.220, J:D.283 NAG-NAG-BMA.21: 7 residues within 4Å: Chain O: K.220, M.223, N.225, Y.243, R.251, S.252, D.283 2 PLIP interactions: 2 interactions with chain O Hydrogen bonds: O:K.220, O:D.283 NAG-NAG-BMA.30: 7 residues within 4Å: Chain T: K.220, M.223, N.225, Y.243, R.251, S.252, D.283 2 PLIP interactions: 2 interactions with chain T Hydrogen bonds: T:K.220, T:D.283 NAG-NAG-BMA.39: 7 residues within 4Å: Chain Y: K.220, M.223, N.225, Y.243, R.251, S.252, D.283 2 PLIP interactions: 2 interactions with chain Y Hydrogen bonds: Y:K.220, Y:D.283

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

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.5: 12 residues within 4Å: Chain B: E.72, S.74, E.159 Chain E: E.121, Q.124, V.125, H.126, I.289, L.295, N.301, I.304, Y.364 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.72, B:S.74 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.14: 12 residues within 4Å: Chain G: E.72, S.74, E.159 Chain J: E.121, Q.124, V.125, H.126, I.289, L.295, N.301, I.304, Y.364 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:E.72, G:S.74 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.23: 12 residues within 4Å: Chain L: E.72, S.74, E.159 Chain O: E.121, Q.124, V.125, H.126, I.289, L.295, N.301, I.304, Y.364 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:E.72, L:S.74 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.32: 12 residues within 4Å: Chain Q: E.72, S.74, E.159 Chain T: E.121, Q.124, V.125, H.126, I.289, L.295, N.301, I.304, Y.364 2 PLIP interactions: 2 interactions with chain Q Hydrogen bonds: Q:E.72, Q:S.74 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.41: 12 residues within 4Å: Chain V: E.72, S.74, E.159 Chain Y: E.121, Q.124, V.125, H.126, I.289, L.295, N.301, I.304, Y.364 2 PLIP interactions: 2 interactions with chain V Hydrogen bonds: V:E.72, V:S.74

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

NAG-NAG-BMA-MAN-MAN.6: 9 residues within 4Å: Chain E: Q.39, Y.41, E.61, D.338, H.339, R.358, Y.386, N.388, S.390 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.41 NAG-NAG-BMA-MAN-MAN.15: 9 residues within 4Å: Chain J: Q.39, Y.41, E.61, D.338, H.339, R.358, Y.386, N.388, S.390 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:Y.41 NAG-NAG-BMA-MAN-MAN.24: 9 residues within 4Å: Chain O: Q.39, Y.41, E.61, D.338, H.339, R.358, Y.386, N.388, S.390 1 PLIP interactions: 1 interactions with chain O Hydrophobic interactions: O:Y.41 NAG-NAG-BMA-MAN-MAN.33: 9 residues within 4Å: Chain T: Q.39, Y.41, E.61, D.338, H.339, R.358, Y.386, N.388, S.390 1 PLIP interactions: 1 interactions with chain T Hydrophobic interactions: T:Y.41 NAG-NAG-BMA-MAN-MAN.42: 9 residues within 4Å: Chain Y: Q.39, Y.41, E.61, D.338, H.339, R.358, Y.386, N.388, S.390 1 PLIP interactions: 1 interactions with chain Y Hydrophobic interactions: Y:Y.41

5 x 906: 1-(2-aminopyridin-4-yl)-3-[(3S)-5-{4-[(E)-(ethoxyimino)methyl]phenoxy}-3-methylpentyl]imidazolidin-2-one(Non-covalent)

906.7: 22 residues within 4Å: Chain A: I.111, D.112, I.113, T.114, F.131, F.135, F.137, Y.153, F.155, P.177, S.178, V.179, V.190, V.192, M.195, Y.201, Q.202, W.203, N.228, M.253, A.275 Chain C: I.24 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:I.111, A:T.114, A:F.131, A:F.135, A:F.135, A:F.155, A:F.155, A:V.179, A:V.192, A:W.203, A:N.228, C:I.24 Hydrogen bonds: A:I.113, A:T.114, A:T.114 pi-Stacking: A:F.135 906.16: 22 residues within 4Å: Chain F: I.111, D.112, I.113, T.114, F.131, F.135, F.137, Y.153, F.155, P.177, S.178, V.179, V.190, V.192, M.195, Y.201, Q.202, W.203, N.228, M.253, A.275 Chain H: I.24 16 PLIP interactions: 15 interactions with chain F, 1 interactions with chain H Hydrophobic interactions: F:I.111, F:T.114, F:F.131, F:F.135, F:F.135, F:F.155, F:F.155, F:V.179, F:V.192, F:W.203, F:N.228, H:I.24 Hydrogen bonds: F:I.113, F:T.114, F:T.114 pi-Stacking: F:F.135 906.25: 22 residues within 4Å: Chain K: I.111, D.112, I.113, T.114, F.131, F.135, F.137, Y.153, F.155, P.177, S.178, V.179, V.190, V.192, M.195, Y.201, Q.202, W.203, N.228, M.253, A.275 Chain M: I.24 16 PLIP interactions: 15 interactions with chain K, 1 interactions with chain M Hydrophobic interactions: K:I.111, K:T.114, K:F.131, K:F.135, K:F.135, K:F.155, K:F.155, K:V.179, K:V.192, K:W.203, K:N.228, M:I.24 Hydrogen bonds: K:I.113, K:T.114, K:T.114 pi-Stacking: K:F.135 906.34: 22 residues within 4Å: Chain P: I.111, D.112, I.113, T.114, F.131, F.135, F.137, Y.153, F.155, P.177, S.178, V.179, V.190, V.192, M.195, Y.201, Q.202, W.203, N.228, M.253, A.275 Chain R: I.24 16 PLIP interactions: 15 interactions with chain P, 1 interactions with chain R Hydrophobic interactions: P:I.111, P:T.114, P:F.131, P:F.135, P:F.135, P:F.155, P:F.155, P:V.179, P:V.192, P:W.203, P:N.228, R:I.24 Hydrogen bonds: P:I.113, P:T.114, P:T.114 pi-Stacking: P:F.135 906.43: 22 residues within 4Å: Chain U: I.111, D.112, I.113, T.114, F.131, F.135, F.137, Y.153, F.155, P.177, S.178, V.179, V.190, V.192, M.195, Y.201, Q.202, W.203, N.228, M.253, A.275 Chain W: I.24 16 PLIP interactions: 1 interactions with chain W, 15 interactions with chain U Hydrophobic interactions: W:I.24, U:I.111, U:T.114, U:F.131, U:F.135, U:F.135, U:F.155, U:F.155, U:V.179, U:V.192, U:W.203, U:N.228 Hydrogen bonds: U:I.113, U:T.114, U:T.114 pi-Stacking: U:F.135

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

NAG.8: 1 residues within 4Å: Chain E: N.21 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.21 NAG.9: 4 residues within 4Å: Chain E: L.192, S.197, N.200, V.205 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:L.192, E:V.205 Hydrogen bonds: E:N.200 NAG.17: 1 residues within 4Å: Chain J: N.21 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:N.21 NAG.18: 4 residues within 4Å: Chain J: L.192, S.197, N.200, V.205 3 PLIP interactions: 3 interactions with chain J Hydrophobic interactions: J:L.192, J:V.205 Hydrogen bonds: J:N.200 NAG.26: 1 residues within 4Å: Chain O: N.21 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:N.21 NAG.27: 4 residues within 4Å: Chain O: L.192, S.197, N.200, V.205 3 PLIP interactions: 3 interactions with chain O Hydrophobic interactions: O:L.192, O:V.205 Hydrogen bonds: O:N.200 NAG.35: 1 residues within 4Å: Chain T: N.21 1 PLIP interactions: 1 interactions with chain T Hydrogen bonds: T:N.21 NAG.36: 4 residues within 4Å: Chain T: L.192, S.197, N.200, V.205 3 PLIP interactions: 3 interactions with chain T Hydrophobic interactions: T:L.192, T:V.205 Hydrogen bonds: T:N.200 NAG.44: 1 residues within 4Å: Chain Y: N.21 1 PLIP interactions: 1 interactions with chain Y Hydrogen bonds: Y:N.21 NAG.45: 4 residues within 4Å: Chain Y: L.192, S.197, N.200, V.205 3 PLIP interactions: 3 interactions with chain Y Hydrophobic interactions: Y:L.192, Y:V.205 Hydrogen bonds: Y:N.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, D. et al., Unexpected mode of engagement between enterovirus 71 and its receptor SCARB2. Nat Microbiol (2019)

Release Date

2018-11-28

Peptides

Polyprotein: AFKPU
Polyprotein: BGLQV
Polyprotein: CHMRW
Polyprotein: DINSX
Lysosome membrane protein 2: EJOTY

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
A

K
A

P
A

U
A

B
B

G
B

L
B

Q
B

V
B

C
C

H
C

M
C

R
C

W
C

D
D

I
D

N
D

S
D

X
D

E
E

J
E

O
E

T
E

Y
E

Polyprotein

Polyprotein

Polyprotein

Polyprotein

Lysosome membrane protein 2

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