SMTL ID : 6wpt.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.70 Å

Oligo State

hetero-3-2-2-mer

Ligands

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.1: 4 residues within 4Å: Chain A: N.736, T.738, L.941, Q.945 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.820, S.822, Q.823 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1117, T.1119, H.1120, F.1122 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.820, S.822, Q.823 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.1117, H.1120, F.1122 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: C.1101, I.1151, V.1152, N.1153 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain C: N.736, L.941 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain C: N.820, S.822 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: N.1117, H.1120, F.1122 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain C: I.1151, N.1153 No protein-ligand interaction detected (PLIP)

1 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.4: 13 residues within 4Å: Chain A: G.358, F.361, N.362, V.386, L.387 Chain F: Y.32, R.98, Y.100, G.112, D.115 Chain G: L.47, Y.50, R.55 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain G Hydrogen bonds: F:Y.32, F:R.98 Hydrophobic interactions: G:L.47, G:Y.50

1 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.12: 14 residues within 4Å: Chain C: G.358, F.361, N.362, V.386, L.387 Chain D: Y.32, R.98, G.112, D.115 Chain E: L.47, Y.50, R.55, T.57, G.58 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:L.47, E:Y.50 Hydrogen bonds: D:Y.32, D:R.98, D:D.115, E:G.58

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

NAG.13: 4 residues within 4Å: Chain A: Y.47, T.48, N.49, N.80 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: N.141, A.142, T.143, N.144 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.253, T.255 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.299, E.300, N.301 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.350, Q.599 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.622 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.635, Q.663 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: H.674, N.676 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.728, G.1150 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: A.725, E.1091, K.1092, N.1093 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: I.1151, V.1152, N.1153 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: F.78, S.79, N.80 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: N.141, A.142, T.143 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.253 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.299, E.300, N.301 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: P.349, N.350, P.598, Q.599 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain B: F.357, G.358, F.361, N.362 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.622 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.635, T.637 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: H.674, N.676 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.728, G.1150 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: N.736, N.938, L.941 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain B: A.725, E.1091, K.1092, N.1093 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.184 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain C: Y.47, T.48, N.49, N.80 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain C: N.141, A.142, T.143, N.144 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: G.251, N.253 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.299, N.301 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: P.349, N.350 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.622, T.623 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.635, T.637 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: H.674, N.676 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: N.728, G.1150 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain C: A.725, E.1091, K.1092, N.1093 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: 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: ABC
S309 neutralizing antibody heavy chain: DF
S309 neutralizing antibody light chain: EG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
D

E
L

G
E

spike glycoprotein

S309 neutralizing antibody heavy chain

S309 neutralizing antibody light chain

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