SMTL ID : 7whd.1

SARS-CoV-2 spike in complex with the ZB8 neutralizing antibody Fab (2u1d)

Coordinates

PDB Format Compare

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: N.691, L.896, Q.1045 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.896 NAG-NAG.2: 3 residues within 4Å: Chain A: N.775, S.777, Q.778 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.1048 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.1072, T.1074, F.1077 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.1108 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.683, G.1105 Chain C: D.770 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.691, L.896, Q.900, Q.1045 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.896 NAG-NAG.8: 2 residues within 4Å: Chain B: N.775, S.777 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: A.680, E.1046, N.1048 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain B: N.1072, T.1074, H.1075, F.1077 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain B: N.1108 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain A: D.770 Chain C: N.683, N.684, G.1105 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain C: N.691, L.896, Q.900, Q.1045 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain C: N.775, S.777 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain C: A.680, N.1048 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain C: N.1072, T.1074, H.1075, F.1077 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 1 residues within 4Å: Chain C: N.1108 No protein-ligand interaction detected (PLIP)

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

NAG.18: 2 residues within 4Å: Chain A: Y.2, N.35 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: E.255, N.256 Chain C: K.532 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: N.577, T.578 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.590, T.592 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.631 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.683 Chain B: D.770 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: N.138, N.139 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.4, N.35 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.256 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.577 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.590 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.631 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: Y.2, N.35 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.96 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: T.82, N.208 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: K.532 Chain C: E.255, N.256 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: N.577, T.578 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.590, T.592 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: H.629, N.631 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.138, N.139 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, B. et al., SARS-CoV-2 hijacks neutralizing dimeric IgA for nasal infection and injury in Syrian hamsters 1 . Emerg Microbes Infect (2023)

Release Date

2023-01-18

Peptides

Spike glycoprotein: ABC
antibody ZB8 heavy chain: DFH
antibody ZB8 light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
G

H
J

E
E

G
H

I
K

Spike glycoprotein

antibody ZB8 heavy chain

antibody ZB8 light chain

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