SMTL ID : 7v23.1

CryoEM structure of del68-76/del679-688 prefusion-stabilized spike in complex with the Fab of N12-9

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

10 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: 6 residues within 4Å: Chain A: N.322, D.569, P.570, Q.571, T.572, L.573 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 8 residues within 4Å: Chain A: F.329, G.330, E.331, V.332, F.333, N.334, S.362, S.364 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.364, A:S.364 NAG-NAG.3: 5 residues within 4Å: Chain A: N.698, F.699, L.903, Q.907, Q.1052 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.782, S.784 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 9 residues within 4Å: Chain A: I.693, A.694, I.695, T.697, Q.1052, E.1053, K.1054, N.1055, F.1056 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.1055 Hydrogen bonds: A:N.1055 NAG-NAG.6: 2 residues within 4Å: Chain B: N.782, S.784 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain B: S.685, A.687, E.1053, N.1055 Chain C: Q.876 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.685 NAG-NAG.8: 5 residues within 4Å: Chain C: T.697, N.698, F.699, L.903, Q.1052 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: N.782, S.784, Q.785 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain A: Q.876 Chain C: A.687, N.1055 No protein-ligand interaction detected (PLIP)

28 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG.11: 1 residues within 4Å: Chain A: N.156 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.273 Chain C: K.549 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: T.298, N.594 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.607, T.609 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.648 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.690 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.1115 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: N.113, F.148 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain B: N.156 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: N.271, E.272, N.273 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: N.322, Q.571 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: F.333, N.334, F.365 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain B: N.594 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.607 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.648 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.690, G.1112 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.698, Q.1052 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.1079, T.1081, H.1082 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.1115 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: N.271, N.273 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: N.322, Q.571 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: F.333, N.334 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.594 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.607 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.648 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.690, G.1112 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain C: N.1079, T.1081, H.1082, F.1084 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.1115 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Du, S. et al., CryoEM structure of del68-76/del679-688 prefusion-stabilized spike in complex with the Fab of N12-9. To Be Published

Release Date

2022-08-10

Peptides

Spike glycoprotein: ABC
the heavy chain of N12-9 Fab: DFH
the light chain of N12-9 Fab: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
O

F
Q

H
S

E
P

G
R

I
T

Spike glycoprotein

the heavy chain of N12-9 Fab

the light chain of N12-9 Fab

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