SMTL ID : 7ls9.1

Cryo-EM structure of neutralizing antibody 1-57 in complex with prefusion SARS-CoV-2 spike glycoprotein

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

3 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.1: 4 residues within 4Å: Chain A: E.132, N.164, N.165 Chain H: N.109 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 4 residues within 4Å: Chain B: N.109 Chain D: E.132, N.164, N.165 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.109 NAG-NAG-BMA.15: 5 residues within 4Å: Chain E: N.109 Chain G: S.112, E.132, N.164, N.165 No protein-ligand interaction detected (PLIP)

18 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: 6 residues within 4Å: Chain A: T.108, N.234, T.236 Chain G: R.457, K.462, E.465 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.801, S.803, Q.804, Q.935 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain A: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain A: I.1132, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain A: N.122, T.124, N.125, V.127 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 7 residues within 4Å: Chain A: R.457, S.459, N.460, K.462, E.465 Chain D: T.108, N.234 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain D: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain D: N.801, S.803, Q.804, Q.935 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain D: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain D: I.1132, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain D: N.122, T.124, N.125, V.127 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.125 NAG-NAG.16: 8 residues within 4Å: Chain D: R.457, S.459, N.460, K.462, E.465 Chain G: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain G: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain G: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 5 residues within 4Å: Chain G: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 2 residues within 4Å: Chain G: I.1132, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain G: N.122, T.124, N.125, V.127 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.125

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

NAG.22: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: F.59, S.60, N.61, P.631 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: N.280, E.281, N.282 Chain G: K.558 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: N.709, G.1131 Chain D: D.796 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain A: N.17, N.137 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: G.339, E.340, N.343 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain D: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain D: F.59, S.60, N.61, P.631 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain A: K.558 Chain D: N.280, E.281, N.282 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain D: N.331, Q.580 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain D: N.709, G.1131 Chain G: D.796 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain D: N.657 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain D: N.616 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain D: N.603 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain D: N.17, N.137 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain D: G.339, E.340, N.343 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain G: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain G: F.59, S.60, N.61, P.631 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain D: K.558 Chain G: N.280, E.281, N.282 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain G: N.331, Q.580 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain A: D.796 Chain G: N.709, G.1131 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain G: N.657 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain G: N.616 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain G: N.603 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain G: N.17, N.137 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain G: G.339, E.340, N.343 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cerutti, G. et al., Structural basis for accommodation of emerging B.1.351 and B.1.1.7 variants by two potent SARS-CoV-2 neutralizing antibodies. Structure (2021)

Release Date

2021-03-17

Peptides

Spike glycoprotein: ADG
1-57 Fab heavy chain: BEH
1-57 Fab light chain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
C

B
H

E
D

H
E

C
L

F
F

I
G

Spike glycoprotein

1-57 Fab heavy chain

1-57 Fab light chain

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