SMTL ID : 7yh7.1

SARS-CoV-2 spike in complex with neutralizing antibody NIV-8 (state 2)

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)(Non-covalent)

NAG-NAG.1: 1 residues within 4Å: Chain B: N.706 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain B: N.790, Q.793 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.706, Q.915 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: N.1087, T.1089, H.1090, F.1092 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain B: N.1123 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain C: N.706, Q.915 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain C: N.790, S.792, Q.793 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain C: N.1087, T.1089, H.1090, F.1092 No protein-ligand interaction detected (PLIP)

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

NAG.9: 2 residues within 4Å: Chain A: Y.17, N.50 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: N.269, E.270, N.271 Chain C: K.547 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: P.319, N.320, Q.569 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.605 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: H.644, N.646 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.698, G.1120 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: A.695, N.1063 Ligand excluded by PLIP NAG.16: 5 residues within 4Å: Chain A: F.327, G.328, F.331, N.332, L.357 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.1087, T.1089, H.1090, F.1092 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.790, S.792, Q.793 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.1123 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.223 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: K.547 Chain B: N.269, E.270, N.271 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: H.644, V.645, N.646 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.698, G.1120 Chain C: D.785 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: N.320, P.568, Q.569 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.605 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: F.327, G.328, F.331, N.332 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: Y.17, N.50 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: N.320, Q.569 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.605 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain C: N.646 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: D.785 Chain C: N.698, G.1120 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.1063 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: E.270, N.271 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain C: F.327, G.328, F.331, N.332 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.1123 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

2023-07-19

Peptides

Spike glycoprotein: ABC
NIV-8 Fab light chain: DFH
NIV-8 Fab heavy chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
Q

F
R

H
U

E
P

G
S

I
V

Spike glycoprotein

NIV-8 Fab light chain

NIV-8 Fab heavy chain

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