SMTL ID : 6wps.1

Structure of the SARS-CoV-2 spike glycoprotein in complex with the S309 neutralizing antibody Fab fragment

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.10 Å

Oligo State

hetero-3-3-3-mer

Ligands

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.1: 5 residues within 4Å: Chain A: N.736, T.738, L.941, Q.945, Q.1090 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.941 NAG-NAG.2: 3 residues within 4Å: Chain A: N.820, S.822, Q.823 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.1117, H.1120, F.1122 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: I.1151, N.1153 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain D: N.736, T.738, L.941, Q.945, Q.1090 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.941 NAG-NAG.7: 3 residues within 4Å: Chain D: N.820, S.822, Q.823 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain D: N.1117, H.1120, F.1122 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain D: I.1151, N.1153 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain G: N.736, T.738, L.941, Q.945, Q.1090 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:L.941 NAG-NAG.12: 3 residues within 4Å: Chain G: N.820, S.822, Q.823 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain G: N.1117, H.1120, F.1122 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain G: I.1151, N.1153 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-FUC.5: 12 residues within 4Å: Chain A: G.358, F.361, N.362, V.386, L.387 Chain B: Y.32, R.98, G.112, D.115 Chain C: Y.50, T.57, G.58 7 PLIP interactions: 1 interactions with chain C, 6 interactions with chain B Hydrogen bonds: C:T.57, B:Y.32, B:Y.32, B:R.98, B:R.98, B:D.115, B:D.115, C:G.58 Hydrophobic interactions: C:Y.50 NAG-NAG-BMA-MAN-MAN-FUC.10: 12 residues within 4Å: Chain D: G.358, F.361, N.362, V.386, L.387 Chain E: Y.32, R.98, G.112, D.115 Chain F: Y.50, T.57, G.58 7 PLIP interactions: 1 interactions with chain F, 6 interactions with chain E Hydrogen bonds: F:T.57, E:Y.32, E:Y.32, E:R.98, E:R.98, E:D.115, E:D.115, F:G.58 Hydrophobic interactions: F:Y.50 NAG-NAG-BMA-MAN-MAN-FUC.15: 12 residues within 4Å: Chain G: G.358, F.361, N.362, V.386, L.387 Chain H: Y.32, R.98, G.112, D.115 Chain I: Y.50, T.57, G.58 7 PLIP interactions: 1 interactions with chain I, 6 interactions with chain H Hydrogen bonds: I:T.57, H:Y.32, H:Y.32, H:R.98, H:R.98, H:D.115, H:D.115, I:G.58 Hydrophobic interactions: I:Y.50

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

NAG.16: 4 residues within 4Å: Chain A: Y.47, T.48, N.49, N.80 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.141, A.142, N.144, V.146 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: T.127, N.253, T.255 Chain D: K.481 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: N.299, E.300, N.301 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: P.349, N.350, P.598, Q.599 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.622 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: N.635, Q.663 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: H.674, N.676 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: N.728, G.1150 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain A: A.725, E.1091, K.1092, N.1093 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: N.184 Chain D: Y.370 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain D: Y.47, T.48, N.49, N.80 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain D: N.141, A.142, N.144, V.146 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain D: T.127, N.253, T.255 Chain G: K.481 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain D: N.299, E.300, N.301 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain D: P.349, N.350, P.598, Q.599 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain D: N.622 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain D: N.635, Q.663 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain D: H.674, N.676 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain D: N.728, G.1150 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain D: A.725, E.1091, K.1092, N.1093 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain D: N.184 Chain G: Y.370 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain G: Y.47, T.48, N.49, N.80 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain G: N.141, A.142, N.144, V.146 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain A: K.481 Chain G: T.127, N.253, T.255 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain G: N.299, E.300, N.301 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain G: P.349, N.350, P.598, Q.599 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain G: N.622 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain G: N.635, Q.663 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain G: H.674, N.676 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain G: N.728, G.1150 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain G: A.725, E.1091, K.1092, N.1093 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain A: Y.370 Chain G: N.184 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pinto, D. et al., Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody. Nature (2020)

Release Date

2020-05-27

Peptides

spike glycoprotein: ADG
S309 neutralizing antibody heavy chain: BEH
S309 neutralizing antibody light chain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
E

B
H

E
C

H
F

C
L

F
D

I
G

spike glycoprotein

S309 neutralizing antibody heavy chain

S309 neutralizing antibody light chain

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