SMTL ID : 7ej4.1

Cryo-EM structure of SARS-CoV-2 spike in complex with a neutralizing antibody RBD-chAb-25

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

27 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: 3 residues within 4Å: Chain A: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.331, I.332, Q.580, T.581 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.616, T.618 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.709, G.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.717, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: S.704, A.706, N.1074 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.706 NAG-NAG.8: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain B: N.234 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain B: N.616, T.618 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain B: S.708, N.709, N.710 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain B: N.717, N.925, Q.1071 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.925 NAG-NAG.15: 2 residues within 4Å: Chain B: N.801, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain B: S.704, A.706, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain C: E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain C: N.331, I.332, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 2 residues within 4Å: Chain C: N.616, T.618 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain A: D.796 Chain C: S.708, N.709, N.710 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 5 residues within 4Å: Chain C: N.717, L.922, N.925, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain C: S.704, A.706, N.1074 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.706 NAG-NAG.26: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 2 residues within 4Å: Chain C: I.1132, N.1134 No protein-ligand interaction detected (PLIP)

21 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG.28: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: N.122, N.125, V.127 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain A: N.164, N.165 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain A: N.234 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain A: G.339, F.342, N.343 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: N.30, F.59, N.61 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.122 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: N.164, N.165 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain B: F.338, G.339, F.342, N.343, L.368 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: V.120, N.122, V.127 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.164, N.165 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: T.108, N.234, T.236 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain C: G.339, F.342, N.343, F.374 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain C: H.655, V.656, N.657 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-25. To be published

Release Date

2021-06-23

Peptides

Spike glycoprotein: ABC
RBD-chAb-25, Heavy chain: DFH
RBD-chAb-25, 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-chAb-25, Heavy chain

RBD-chAb-25, Light chain

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