SMTL ID : 8hhy.1

SARS-CoV-2 Delta Spike in complex with IS-9A

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

4 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 G: N.805, S.807, Q.808 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain H: N.335, T.337, N.338, Q.584 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:N.335 NAG-NAG.3: 3 residues within 4Å: Chain H: N.805, S.807, Q.808 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain I: N.721, Q.930, S.933 No protein-ligand interaction detected (PLIP)

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

NAG.5: 2 residues within 4Å: Chain G: N.335, Q.584 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain G: N.620, T.622, Q.648 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain G: N.713, G.1135 Chain H: D.800 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain G: A.710, K.1077, N.1078 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain G: V.126, N.128, K.135 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain G: I.1136, N.1138 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain G: N.1102, T.1104, H.1105, F.1107 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain G: N.721, F.722, L.926, Q.930 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain H: Y.34, N.67 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain H: N.620, T.622 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain H: N.713 Chain I: I.798, D.800 Ligand excluded by PLIP NAG.16: 5 residues within 4Å: Chain H: V.126, N.128, N.131, V.133, L.147 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain H: N.286 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain H: N.1102, T.1104, H.1105, F.1107 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain H: A.710, N.1078 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain H: N.721, L.926 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain I: N.620, T.622, Q.648 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain G: I.798, D.800 Chain I: N.713, I.1134, G.1135 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain I: N.335, T.337, T.585 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain I: V.126, N.128, V.133, K.135 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain I: A.710, S.715, N.1078 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain I: N.1102, T.1104, H.1105 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain I: I.1136, N.1138 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain I: N.805, S.807, Q.808 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, K.A. et al., Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2. Nat Commun (2023)

Release Date

2023-02-01

Peptides

IS-9A Fab heavy chain: ACE
IS-9A Fab light chain: BDF
Spike glycoprotein: GHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

C
G

E
H

B
W

D
I

F
L

G
A

H
B

I
C

IS-9A Fab heavy chain

IS-9A Fab light chain

Spike glycoprotein

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