SMTL ID : 7ej5.1

Cryo-EM structure of SARS-CoV-2 spike in complex with a neutralizing antibody RBD-chAb-45

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

24 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: E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.709, G.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain A: A.706, N.1074 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.706 NAG-NAG.7: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain B: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: S.708, N.709, N.710 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain B: N.717, L.922 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain B: S.704, A.706, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain B: N.1098, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain C: E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain C: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain C: N.616, T.618 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain C: N.709 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain C: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain C: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.25: 3 residues within 4Å: Chain A: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: N.122, N.125, V.127 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: N.164, N.165 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain A: N.234 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: G.339, F.342, N.343 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.34: 6 residues within 4Å: Chain B: V.120, N.122, T.124, N.125, V.127, Y.160 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: N.164, N.165 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: G.232, I.233, N.234 Ligand excluded by PLIP NAG.37: 6 residues within 4Å: Chain B: F.342, N.343, S.371, S.373, F.374, W.436 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.122, T.124 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: S.112, N.164, N.165 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.234 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain C: G.339, N.343, S.371, S.373, F.374 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: A.706, N.1074 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, T.J. et al., Cryo-EM structure of SARS-CoV-2 spike in complex with a neutralizing antibody RBD-chAb-45. To Be Published

Release Date

2021-06-23

Peptides

Spike glycoprotein: ABC
RBD-chAb45, Heavy chain: DFH
RBD-chAb45, Light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
I

H
J

E
L

G
M

I
N

Spike glycoprotein

RBD-chAb45, Heavy chain

RBD-chAb45, Light chain

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