SMTL ID : 7wuh.1

SARS-CoV-2 Spike in complex with Fab of m31A7

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

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

NAG-NAG-FUC.1: 5 residues within 4Å: Chain A: S.99, K.100, N.151, N.152, I.220 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.151, B:R.342 NAG-NAG-FUC.19: 1 residues within 4Å: Chain C: N.136 No protein-ligand interaction detected (PLIP)

8 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: 2 residues within 4Å: Chain A: T.95, N.221 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.704, N.906, L.909 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: N.788, S.790, Q.791 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.791 NAG-NAG.7: 8 residues within 4Å: Chain A: V.107, N.109, N.112, V.113, V.114, V.158, S.159, Q.160 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.158 NAG-NAG.9: 3 residues within 4Å: Chain B: H.133, K.134, N.136 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 6 residues within 4Å: Chain B: N.109, N.112, V.114, K.137, V.158, S.159 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.158 NAG-NAG.13: 3 residues within 4Å: Chain A: D.783 Chain B: N.696, G.1118 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.783 NAG-NAG.15: 3 residues within 4Å: Chain B: K.782, N.788, S.790 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN: 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.3: 1 residues within 4Å: Chain A: N.269 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.16: 1 residues within 4Å: Chain B: N.269 No protein-ligand interaction detected (PLIP)

4 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.4: 3 residues within 4Å: Chain A: N.318, Q.567, T.568 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 5 residues within 4Å: Chain A: N.690, S.691, V.692, N.1061, F.1062 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.691 NAG-NAG-BMA.17: 2 residues within 4Å: Chain A: K.545 Chain C: N.269 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 2 residues within 4Å: Chain C: N.788, S.790 No protein-ligand interaction detected (PLIP)

2 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.10: 4 residues within 4Å: Chain B: N.318, I.319, Q.567, T.568 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.14: 1 residues within 4Å: Chain B: N.704 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: 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.12: 8 residues within 4Å: Chain B: Q.102, E.119, N.151, N.152, T.154 Chain C: R.453, I.455, S.456 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.456

2 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.18: 3 residues within 4Å: Chain C: N.704, T.706, Q.913 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Q.913 NAG-NAG-BMA-FUC.24: 8 residues within 4Å: Chain F: N.119, Y.120 Chain G: K.56, Y.75, W.76, S.79, R.80, E.81 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:K.56, G:R.80

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.20: 2 residues within 4Å: Chain C: E.296, N.590 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- NAG- MAN: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]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-NAG-MAN.21: 4 residues within 4Å: Chain C: N.318, I.319, Q.567, T.568 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.567, C:T.568

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN.23: 7 residues within 4Å: Chain B: Q.882 Chain C: E.689, N.690, S.691, V.692, E.1059, N.1061 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.691

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

NAG.25: 1 residues within 4Å: Chain A: N.644 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: N.696, N.697, G.1118 Chain C: D.783 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: F.1062, N.1085, T.1087 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: Y.15, N.48 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain A: N.523, N.603 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: Y.15, N.48 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: N.183, G.186, I.220, N.221 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: K.841 Chain B: N.603 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.61, T.63 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: N.590, T.591 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: H.642, V.643, N.644 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.1061, F.1062 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain B: K.1060, N.1085, F.1090, Y.1097 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: K.1060, N.1085, Y.1097 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: A.14, Y.15, T.16, N.48 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain C: S.99, E.119, N.151, N.152 Ligand excluded by PLIP NAG.41: 5 residues within 4Å: Chain C: N.109, A.110, T.111, V.113, S.159 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.221 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain H: Y.118, N.119, Y.120 Chain I: Y.75, W.76 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, H.Y. et al., Vaccination with SARS-CoV-2 spike protein lacking glycan shields elicits enhanced protective responses in animal models. Sci Transl Med (2022)

Release Date

2022-03-23

Peptides

Spike glycoprotein: ABC
m31A7 Fab heavy chain: DFH
m31A7 Fab light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
D

F
H

H
K

E
F

G
I

I
L

Spike glycoprotein

m31A7 Fab heavy chain

m31A7 Fab light chain

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