SMTL ID : 7tat.1

SARS-CoV-2 spike in complex with the S2K146 neutralizing antibody Fab fragment (two receptor-binding domains open)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

8 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.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.1098, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.717, L.922, Q.926 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.4: 2 residues within 4Å: Chain B: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.1098, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.717, L.922, Q.926 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG.7: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain C: I.1132, N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.9: 1 residues within 4Å: Chain A: N.165 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: I.233, N.234 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: H.655, V.656, N.657 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 Chain B: Q.895 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain A: F.338, G.339, F.342, N.343, L.368 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: Y.28, N.61 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: N.280, N.282 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.616, Q.644 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: V.656, N.657 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.709, G.1131 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain B: A.706, E.1072, K.1073, N.1074 Chain C: Q.895 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.165 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.122, A.123 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: F.342, N.343 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 C: Y.28, N.61 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.616, Q.644 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: H.655, V.656, N.657 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.801, S.803 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain C: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.122, A.123 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.234 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.280, N.282 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: N.1098, H.1101, F.1103 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, Y.J. et al., Antibody-mediated broad sarbecovirus neutralization through ACE2 molecular mimicry. Science (2022)

Release Date

2022-01-12

Peptides

Spike glycoprotein: ABC
S2K146 Fab heavy chain: DFH
S2K146 Fab light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
D

H
F

E
L

G
E

I
G

Spike glycoprotein

S2K146 Fab heavy chain

S2K146 Fab light chain

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