SMTL ID : 8dlz.1

Cryo-EM structure of SARS-CoV-2 D614G spike protein in complex with VH ab6

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-mer

Ligands

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.1: 3 residues within 4Å: Chain A: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 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.3: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 NAG-NAG.15: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.19: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: N.122, T.124, N.125, V.127 Ligand excluded by PLIP NAG.21: 5 residues within 4Å: Chain A: E.132, N.164, N.165 Chain D: K.64, S.65 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: T.108, N.234 Chain C: E.465 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: N.280, E.281, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: N.709, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain B: N.122, T.124, N.125, V.127, F.157 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: E.132, N.164, N.165 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: T.108, N.234, T.236 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.280, N.282 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain C: N.122, T.124, V.127, F.157 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: E.132, N.164, N.165 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: T.108, N.234, T.236 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.331, Q.580, L.582 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: F.338, G.339, N.343 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, G.1131 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mannar, D. et al., SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization. Nat Commun (2022)

Release Date

2022-08-31

Peptides

Spike glycoprotein: ABC
VH ab6: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

Spike glycoprotein

VH ab6

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