SMTL ID : 7fae.1

S protein of SARS-CoV-2 in complex bound with P36-5D2(state2)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

17 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: F.342, N.343, S.371 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.371 NAG-NAG.2: 2 residues within 4Å: Chain A: N.709 Chain B: D.796 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: N.717, L.922, N.925, Q.926, Q.1071 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.922, A:N.925 NAG-NAG.4: 2 residues within 4Å: Chain A: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, G.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: N.717, L.922, Q.926 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 NAG-NAG.10: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 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.14: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain B: N.1098, T.1100, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP)

28 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-functional Binders)

NAG.18: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: N.122, N.125, V.127, F.157 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: N.165 Chain H: R.121 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.234 Chain C: R.466 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: E.281, N.282 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.122, T.124, V.127 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: E.132, N.165 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: G.232, N.234 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.603, T.604 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain B: N.709, I.1130, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: N.122, T.124, V.127, K.129 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.164, N.165 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.234 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: G.339, N.343 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain C: A.706, E.1072, K.1073, N.1074 Ligands: NAG.45 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Ligands: NAG.44 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shan, S. et al., A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants. Front Immunol (2021)

Release Date

2021-12-22

Peptides

Spike glycoprotein: ABC
P36-5D2 heavy chain: DFH
P36-5D2 light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
e

H
h

E
d

G
g

I
L

Spike glycoprotein

P36-5D2 heavy chain

P36-5D2 light chain

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