SMTL ID : 8cin.1

BA.4/5-5 FAB IN COMPLEX WITH SARS-COV-2 BA.4 SPIKE GLYCOPROTEIN

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: 4 residues within 4Å: Chain A: N.693, L.898, Q.902, Q.1047 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.898 NAG-NAG.2: 3 residues within 4Å: Chain A: N.777, S.779, Q.780 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1074, T.1076, H.1077, F.1079 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.1110 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: N.693, L.898, Q.902, Q.1047 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.898 NAG-NAG.6: 3 residues within 4Å: Chain B: N.777, S.779, Q.780 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.1074, T.1076, H.1077, F.1079 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.1110 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: N.693, L.898, Q.902, Q.1047 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.898 NAG-NAG.10: 3 residues within 4Å: Chain C: N.777, S.779, Q.780 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: N.1074, T.1076, H.1077, F.1079 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain C: N.1110 No protein-ligand interaction detected (PLIP)

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

NAG.13: 3 residues within 4Å: Chain A: Y.4, N.6, N.37 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.256, E.257, N.258 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.579, T.580 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.592 Chain C: I.810, Q.812 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: Y.631, N.633 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.685 Chain C: I.770, Y.772 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: A.682, E.1048, N.1050 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: N.307, S.506, Q.556 Chain I: K.54 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.319 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: Y.4, N.6, N.37 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.256, E.257, N.258 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.579, T.580 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: I.810, Q.812 Chain B: N.592 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: Y.631, N.633 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: I.770, Y.772 Chain B: N.685 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: A.682, E.1048, N.1050 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain B: N.307, S.506, Q.556 Chain E: K.54 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.319 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: Y.4, N.6, N.37 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: N.256, E.257, N.258 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.579, T.580 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: I.810, Q.812 Chain C: N.592 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: Y.631, N.633 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: I.770, Y.772 Chain C: N.685 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: A.682, E.1048, N.1050 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain C: N.307, S.506, Q.556 Chain H: K.54 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain C: N.319 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, D. et al., The SARS-CoV-2 neutralizing antibody response to SD1 and its evasion by BA.2.86. Nat Commun (2024)

Release Date

2024-02-21

Peptides

Spike glycoprotein: ABC
BA.4/5-5 fab HEAVY CHAIN: DFG
BA.4/5-5 fab LIGHT CHAIN: EHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

F
H

G
J

E
F

H
K

I
L

Spike glycoprotein

BA.4/5-5 fab HEAVY CHAIN

BA.4/5-5 fab LIGHT CHAIN