SMTL ID : 7swx.1

SARS-CoV-2 Spike in complex with neutralizing Fab SARS2-57 (three down conformation)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-mer

Ligands

28 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: 2 residues within 4Å: Chain A: N.152 Chain C: I.455 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 8 residues within 4Å: Chain A: T.95, N.221, T.223 Chain C: R.444, K.445, S.446, N.447, K.449 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.445, C:S.446, C:S.446 NAG-NAG.3: 2 residues within 4Å: Chain A: N.330, S.358 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.603, T.605, Q.631 Chain B: Q.823 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: C.2, N.4, N.124 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.330, V.354, S.358 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain B: N.603, T.632 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: A.693, E.1059, N.1061 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain B: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: C.2, N.4, N.124 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain A: I.821 Chain C: N.603, T.605, T.632, R.633 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain C: N.788, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain C: A.693, E.1059, N.1061 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 1 residues within 4Å: Chain C: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain A: N.318, Q.567, L.569 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain A: N.704, Q.913, Q.1058 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.913 NAG-NAG.20: 2 residues within 4Å: Chain A: A.693, N.1061 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain A: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain B: N.704, L.909, Q.1058 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.909 NAG-NAG.23: 3 residues within 4Å: Chain B: N.1085, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 2 residues within 4Å: Chain C: N.318, Q.567 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 2 residues within 4Å: Chain C: N.704, Q.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain C: N.1085, T.1087, H.1088, F.1090 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.1088 NAG-NAG.27: 2 residues within 4Å: Chain B: N.318, Q.567 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 4 residues within 4Å: Chain C: N.330, V.354, L.355, S.358 No protein-ligand interaction detected (PLIP)

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

NAG.29: 2 residues within 4Å: Chain A: N.4, N.124 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain A: Y.15, N.17, N.48 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: N.112, V.114, V.158 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: H.133, N.136 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain A: N.590 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: H.642, N.644 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain A: N.696, I.1117, G.1118 Chain B: D.783 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.48 Ligand excluded by PLIP NAG.37: 5 residues within 4Å: Chain B: N.109, T.111, N.112, V.114, E.141 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain B: N.136 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain A: Y.338, I.455 Chain B: N.151, N.152 Ligand excluded by PLIP NAG.40: 7 residues within 4Å: Chain A: R.444, N.447, K.449, E.452 Chain B: T.95, N.221, T.223 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain A: K.545 Chain B: E.268, N.269 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain B: N.590 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain B: N.644 Ligand excluded by PLIP NAG.44: 6 residues within 4Å: Chain B: N.696, I.1117, G.1118 Chain C: D.783, G.785, P.886 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: Y.15, N.48 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain C: N.109, T.111, N.112, V.114 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain C: N.135, N.136, M.140 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain B: Y.338, I.455 Chain C: N.151, N.152 Ligand excluded by PLIP NAG.49: 7 residues within 4Å: Chain B: R.444, N.447, K.449, E.452 Chain C: T.95, N.221, T.223 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain C: N.267, N.269, T.273 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain C: N.590 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain C: H.642, N.644 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain A: D.783, P.886 Chain C: N.696, I.1117 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Adams, L.J. et al., A broadly reactive antibody targeting the N-terminal domain of SARS-CoV-2 spike confers Fc-mediated protection. Cell Rep Med (2023)

Release Date

2022-11-23

Peptides

Spike glycoprotein: ABC
SARS2-57 Fv heavy chain: D
SARS2-57 Fv light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
L

Spike glycoprotein

SARS2-57 Fv heavy chain

SARS2-57 Fv light chain

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