SMTL ID : 7t3m.1

SARS-CoV-2 S (Spike Glycoprotein) D614G with Three (3) RBDs Up, Bound to Antibody 2-7 scFv, composite map

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

3 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: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.2: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG.3: 4 residues within 4Å: Chain D: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.922

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

NAG.4: 2 residues within 4Å: Chain A: N.30, N.61 Ligand excluded by PLIP NAG.5: 6 residues within 4Å: Chain A: N.122, T.124, N.125, V.126, V.127, V.171 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.164, N.165 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.234 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: E.281, N.282 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: F.338, G.339, N.343 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain A: S.708, N.709, N.710 Chain D: I.794, D.796 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.1074 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.30, N.61 Ligand excluded by PLIP NAG.20: 6 residues within 4Å: Chain B: N.122, T.124, N.125, V.126, V.127, V.171 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: N.164, N.165 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.234 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: F.338, G.339, N.343 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain A: I.794, D.796 Chain B: S.708, N.709, N.710 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.1074 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain D: N.30, N.61 Ligand excluded by PLIP NAG.35: 6 residues within 4Å: Chain D: N.122, T.124, N.125, V.126, V.127, V.171 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain D: N.164, N.165 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain D: N.234 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain D: E.281, N.282 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain D: N.331, Q.580 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain D: F.338, G.339, N.343 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain D: N.603 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain D: N.616 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain D: H.655, N.657 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain B: I.794, D.796 Chain D: S.708, N.709, N.710 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain D: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain D: N.1074 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain D: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain D: N.1134 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Byrne, P.O. et al., SARS CoV-2 S (Spike Glycoprotein) D614G with Three (3) RBDs Up, Bound to Antibody 2-7 scFv. To Be Published

Release Date

2022-08-24

Peptides

Spike glycoprotein: ABD
Antibody 2-7 scFv, variable heavy chain VH: CEF
Antibody 2-7 scFv, variable light chain VL: GHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

D
G

C
D

E
H

F
I

G
J

H
K

I
L

Spike glycoprotein

Antibody 2-7 scFv, variable heavy chain VH

Antibody 2-7 scFv, variable light chain VL

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