SMTL ID : 8cim.1

BA.2-07 FAB IN COMPLEX WITH SARS-COV-2 BA.2.12.1 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: 3 residues within 4Å: Chain A: N.714, L.919, Q.1068 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.919 NAG-NAG.2: 4 residues within 4Å: Chain A: N.798, S.800, Q.801, Q.932 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 B: N.714, L.919, Q.1068 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.919 NAG-NAG.6: 4 residues within 4Å: Chain B: N.798, S.800, Q.801, Q.932 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 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.9: 3 residues within 4Å: Chain C: N.714, L.919, Q.1068 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.919 NAG-NAG.10: 4 residues within 4Å: Chain C: N.798, S.800, Q.801, Q.932 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP)

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

NAG.13: 3 residues within 4Å: Chain A: Y.25, N.27, N.58 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.277, E.278, N.279 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: K.307, N.600, T.601 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: N.613, Q.641 Chain C: I.831, Q.833 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: Y.652, N.654 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.706 Chain C: Y.793 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: A.703, E.1069, K.1070, N.1071 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: N.328, Q.577 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: Y.25, N.27, N.58 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.277, E.278, N.279 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: K.307, N.600, T.601 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: I.831, Q.833 Chain B: N.613, Q.641 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: Y.652, N.654 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: Y.793 Chain B: N.706 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain B: A.703, E.1069, K.1070, N.1071 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.328, Q.577 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: Y.25, N.27, N.58 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: N.277, E.278, N.279 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: K.307, N.600, T.601 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain B: I.831, Q.833 Chain C: N.613, Q.641 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: Y.652, N.654 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: Y.793 Chain C: N.706 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain C: A.703, E.1069, K.1070, N.1071 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.328, Q.577 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duyvesteyn, H.M.E. et al., Isolation of a pair of potent broadly neutralizing mAb binding to RBD and SD1 domains of SARS-CoV-2. Res Sq (2023)

Release Date

2023-07-05

Peptides

Spike glycoprotein,Fibritin: ABC
BA.2-07 FAB HEAVY CHAIN: DFH
BA.2-07 FAB LIGHT CHAIN: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
F

H
H

E
E

G
G

I
L

Spike glycoprotein,Fibritin

BA.2-07 FAB HEAVY CHAIN

BA.2-07 FAB LIGHT CHAIN

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