SMTL ID : 7d0b.1

S protein of SARS-CoV-2 in complex bound with P5A-3C12_1B

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-mer

Ligands

21 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: 2 residues within 4Å: Chain A: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: F.342, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 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.4: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 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: 3 residues within 4Å: Chain A: N.1098, T.1100, 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: 4 residues within 4Å: Chain B: N.331, P.579, Q.580, L.582 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.582 Hydrogen bonds: B:Q.580 NAG-NAG.9: 3 residues within 4Å: Chain B: N.709, G.1131 Chain C: D.796 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 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.11: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain C: N.331, P.579, Q.580, L.582 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.582 Hydrogen bonds: C:Q.580 NAG-NAG.15: 2 residues within 4Å: Chain A: D.796 Chain C: N.709 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 5 residues within 4Å: Chain C: N.717, L.922, N.925, Q.926, Q.1071 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.922, C:N.925 NAG-NAG.17: 2 residues within 4Å: Chain C: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain B: A.706, E.1072, K.1073, N.1074 No protein-ligand interaction detected (PLIP)

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

NAG.22: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: N.122, T.124, V.127 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: E.132, N.165 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: G.232, N.234 Chain C: E.465 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: N.280, E.281, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: N.603, T.604 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain A: N.709, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: N.122, T.124, V.127 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: E.132, N.165 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: G.232, N.234 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: F.338, G.339, N.343 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: N.603, T.604 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: N.122, T.124, V.127 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: E.132, N.165 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain B: K.462, E.465 Chain C: N.234 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain B: K.558 Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: F.338, G.339, N.343 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: N.603, T.604 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, R. et al., Structural basis for bivalent binding and inhibition of SARS-CoV-2 infection by human potent neutralizing antibodies. Cell Res. (2021)

Release Date

2021-03-10

Peptides

Spike glycoprotein: ABC
Heavy chain of P5A-3C12: D
Light chain of P5A-3C12: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
L

Spike glycoprotein

Heavy chain of P5A-3C12

Light chain of P5A-3C12

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