SMTL ID : 5xbm.1

Structure of SCARB2-JL2 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

hetero-2-2-2-mer

Ligands

3 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: 5 residues within 4Å: Chain C: N.32, V.50, L.96, R.98, T.134 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.7: 5 residues within 4Å: Chain F: N.32, V.50, L.96, R.98, T.134 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.12: 8 residues within 4Å: Chain F: Q.27, Y.29, E.49, E.325, D.326, R.346, N.376, S.378 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.325 Hydrophobic interactions: F:Y.29

6 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 C: L.58, Y.81, V.82, W.142, N.170 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.58 NAG-NAG.3: 7 residues within 4Å: Chain C: K.208, C.209, M.211, N.213, Y.231, S.240, F.275 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.208 NAG-NAG.4: 4 residues within 4Å: Chain C: N.268, C.282, L.283, G.284 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 7 residues within 4Å: Chain F: Y.55, L.58, A.80, Y.81, V.82, W.142, N.170 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:L.58 NAG-NAG.9: 7 residues within 4Å: Chain F: K.208, C.209, M.211, N.213, Y.231, S.240, F.275 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:K.208 NAG-NAG.10: 4 residues within 4Å: Chain F: N.268, L.283, G.284, R.312 No protein-ligand interaction detected (PLIP)

3 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.5: 9 residues within 4Å: Chain C: V.113, H.114, I.277, P.278, N.281, L.283, N.289, I.292, Y.352 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.6: 8 residues within 4Å: Chain C: Q.27, Y.29, E.49, D.326, R.346, Y.374, N.376, S.378 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.29 NAG-NAG-BMA-MAN-MAN.11: 7 residues within 4Å: Chain F: V.113, H.114, I.277, L.283, N.289, S.291, Y.352 No protein-ligand interaction detected (PLIP)

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

NAG.13: 4 residues within 4Å: Chain C: L.180, D.184, S.185, N.188 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.180 Hydrogen bonds: C:D.184, C:N.188 NAG.14: 4 residues within 4Å: Chain F: L.180, D.184, L.187, N.188 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:L.180 Hydrogen bonds: F:D.184

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, X. et al., The binding of a monoclonal antibody to the apical region of SCARB2 blocks EV71 infection. Protein Cell (2017)

Release Date

2018-06-27

Peptides

light chain of JL2: AD
heavy chain of JL2: BE
Lysosome membrane protein 2: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

light chain of JL2

heavy chain of JL2

Lysosome membrane protein 2

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