SMTL ID : 8hgl.1

SARS-CoV-2 spike in complex with neutralizing antibody NIV-11

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

12 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: 5 residues within 4Å: Chain A: F.338, G.339, F.342, N.343, V.367 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.367 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 A: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain D: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain D: F.338, G.339, F.342, N.343, V.367 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.367 NAG-NAG.7: 3 residues within 4Å: Chain D: N.717, L.922, Q.926 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.922 NAG-NAG.8: 2 residues within 4Å: Chain D: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain G: N.331, P.579, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain G: F.338, G.339, F.342, N.343, V.367 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:V.367 NAG-NAG.11: 3 residues within 4Å: Chain G: N.717, L.922, Q.926 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:L.922 NAG-NAG.12: 2 residues within 4Å: Chain G: N.801, S.803 No protein-ligand interaction detected (PLIP)

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

NAG.13: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.122, N.125 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.165 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: G.232, I.233, N.234 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: H.655, V.656, N.657 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain D: E.281, N.282 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain D: Y.28, N.61 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain D: N.122, N.125 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain D: N.165 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain D: I.233, N.234 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain D: N.603 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain D: N.616, T.618 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain D: H.655, V.656, N.657 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain D: N.709, G.1131 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain D: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain D: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain D: N.1134 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain G: N.280, E.281, N.282 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain G: Y.28, N.61 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain G: N.122, N.125, V.127 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain G: N.165 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain D: H.519 Chain G: N.234 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain G: N.603 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain G: N.616 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain G: H.655, V.656, N.657 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain G: N.709, G.1131 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain G: E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain G: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain G: N.1134 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moriyama, S. et al., Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants. Nat Commun (2023)

Release Date

2023-10-25

Peptides

Spike glycoprotein: ADG
NIV-11 Fab heavy chain: BEH
NIV-11 Fab light chain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
E

B
H

E
C

H
F

C
L

F
D

I
G

Spike glycoprotein

NIV-11 Fab heavy chain

NIV-11 Fab light chain

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