SMTL ID : 7d03.1

S protein of SARS-CoV-2 in complex bound with FabP5A-2G7

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-mer

Ligands

20 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)

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

NAG.21: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: N.122, T.124, V.127 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: E.132, N.165 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: G.232, N.234 Chain C: E.465 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain A: N.280, E.281, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: N.603, T.604 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: N.709, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: N.122, T.124, V.127 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: E.132, N.165 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: G.232, N.234 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: F.338, G.339, N.343 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.603, T.604 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain B: A.706, E.1072, K.1073, N.1074 Ligands: NAG.40 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Ligands: NAG.39 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.122, T.124, V.127 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: E.132, N.165 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain B: K.462, E.465 Chain C: N.234 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain B: K.558 Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: F.338, G.339, N.343 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: N.603, T.604 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.49: 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
Immunoglobulin heavy variable 4-61,chain H of FabP5A-2G7,Epididymis luminal protein 214: D
IGL c2312_light_IGLV2-14_IGLJ2,IGL@ protein: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
L

Spike glycoprotein

Immunoglobulin heavy variable 4-61,chain H of FabP5A-2G7,Epididymis luminal protein 214

IGL c2312_light_IGLV2-14_IGLJ2,IGL@ protein

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