SMTL ID : 8hhx.1

SARS-CoV-2 Delta Spike in complex with FP-12A

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

7 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.721, L.926, Q.930 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.805, S.807, Q.808 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain B: N.721 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain C: N.721, Q.930 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain C: N.805 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain C: N.1102, T.1104, H.1105, F.1107, I.1118 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain A: A.710, E.1076, K.1077, N.1078 No protein-ligand interaction detected (PLIP)

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

NAG.8: 2 residues within 4Å: Chain A: N.335, Q.584 Ligand excluded by PLIP NAG.9: 5 residues within 4Å: Chain A: N.128, A.129, N.131, G.162, V.163 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.661 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.620 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.713 Chain C: I.798, D.800 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.1138 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain B: N.805, S.807, Q.808 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain B: N.1102, T.1104, H.1105, F.1107 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain B: N.1138 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: N.284, N.286 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.607 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.620, T.622 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: N.713, G.1135, I.1136 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.1078 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain C: Y.34, N.67 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: K.562 Chain C: N.284, E.285, N.286 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain C: N.607 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain C: N.620, T.622 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain C: H.659, N.661 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: N.713, N.714 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: Q.899 Chain C: A.710, N.1078 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

Spike glycoprotein: ABC
FP-12A Fab heavy chain: DF
FP-12A Fab light chain: EG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
F

F
H

E
G

G
I

Spike glycoprotein

FP-12A Fab heavy chain

FP-12A Fab light chain

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