SMTL ID : 7yeg.1

SARS-CoV-2 Spike (6P) in complex with 3 R1-32 Fabs and 3 ACE2

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

6 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 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP)

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

NAG.7: 1 residues within 4Å: Chain A: N.282 Ligand excluded by PLIP NAG.8: 5 residues within 4Å: Chain A: N.331, I.332, Q.580, T.581, L.582 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.709, N.710 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: N.1098, T.1100, F.1103, Y.1110 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain B: N.282 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain B: N.331, I.332, P.579, Q.580 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: N.709, N.710 Chain C: D.796 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain B: N.1098, T.1100, F.1103, Y.1110 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: K.557, K.558 Chain C: N.282 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain C: N.331, I.332, P.579, Q.580 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: N.709, N.710 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain C: N.1098, T.1100, F.1103, Y.1110 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain D: N.35, T.37 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain D: Q.71, N.72, T.74 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain D: N.304 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain D: F.296, S.299, S.402, S.527, N.528 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain I: T.34, N.35, T.37 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain I: N.72, T.74 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain I: E.294, N.304 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain I: F.296, S.299, S.402, S.527, N.528 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain J: T.34, N.35, T.37 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain J: Q.71, N.72, T.74 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain J: E.294, N.304 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain J: F.296, S.299, S.402, S.527, N.528 Ligand excluded by PLIP

3 x ZN: ZINC ION(Non-covalent)

ZN.31: 4 residues within 4Å: Chain D: H.356, E.357, H.360, E.384 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.357, D:H.360, D:E.384 ZN.36: 3 residues within 4Å: Chain I: H.356, H.360, E.384 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:H.356, I:H.360, I:E.384 ZN.41: 3 residues within 4Å: Chain J: H.356, H.360, E.384 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:H.356, J:H.360, J:E.384

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, P. et al., SARS-CoV-2 Delta and Omicron variants evade population antibody response by mutations in a single spike epitope. Nat Microbiol (2022)

Release Date

2022-08-24

Peptides

Spike glycoprotein: ABC
Angiotensin-converting enzyme 2: DIJ
heavy chain of R1-32 Fab: EGK
light chain of R1-32 Fab: FHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

I
J

J
M

E
H

G
G

K
N

F
L

H
I

L
O

Spike glycoprotein

Angiotensin-converting enzyme 2

heavy chain of R1-32 Fab

light chain of R1-32 Fab

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