SMTL ID : 7q9m.1

Beta-53 fab in complex with SARS-CoV-2 beta-Spike glycoprotein

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 7 residues within 4Å: Chain A: G.336, F.339, N.340, V.364 Chain F: N.28, V.101, A.102 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 7 residues within 4Å: Chain C: G.336, F.339, N.340, V.364 Chain D: N.28, V.101, A.102 No protein-ligand interaction detected (PLIP)

11 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 3 residues within 4Å: Chain A: N.714, L.919, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 9 residues within 4Å: Chain B: G.336, F.339, N.340, V.364, L.365 Chain H: N.28, V.101, A.102, L.103 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: N.714, L.919, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP)

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

NAG.14: 1 residues within 4Å: Chain A: N.279 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.328, Q.577 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.613, T.615 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.706, G.1128 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: A.703, E.1069, N.1071 Chain B: Q.892 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: N.714, L.919, Q.923 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.279 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: N.613, T.615 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: H.652, N.654 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.706, G.1128 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain C: N.613 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain C: N.654 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: D.793 Chain C: N.706, G.1128 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain C: A.703, E.1069, K.1070, N.1071 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, C. et al., The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. Cell Host Microbe (2022)

Release Date

2021-12-15

Peptides

Spike glycoprotein: ABC
Beta-53 fab heavy chain: DFH
Beta-53 fab light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
J

H
E

E
L

G
K

I
F

Spike glycoprotein

Beta-53 fab heavy chain

Beta-53 fab light chain

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