SMTL ID : 8zhn.1

SARS-CoV-2 spike trimer (6P) in complex with three H18 and three R1-32 Fabs (one RBD rotated)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-3-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.707, L.912, Q.916, Q.1061 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.791, S.793, Q.794 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1088, T.1090, H.1091, F.1093 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.1124 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain F: N.707, L.912, Q.916, Q.1061 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain F: N.791, S.793, Q.794 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain F: N.1088, T.1090, H.1091, F.1093 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain F: N.1124 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain G: N.707, L.912, Q.916, Q.1061 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain G: N.791, S.793, Q.794 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain G: N.1088, T.1090, H.1091, F.1093 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain G: N.1124 No protein-ligand interaction detected (PLIP)

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

NAG.13: 1 residues within 4Å: Chain A: N.51 Ligand excluded by PLIP NAG.14: 6 residues within 4Å: Chain A: V.110, N.112, T.114, N.115, V.117, F.147 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: Q.105, N.155, T.157 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.224 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: E.271, N.272 Chain G: K.548 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain A: N.321, P.517, K.518, T.521, Q.570 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.333 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.606 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: H.645, N.647 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.699 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain A: N.1064 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain F: Y.18, N.51 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain F: N.112, T.114, V.117, F.147 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain F: E.122, N.154, N.155 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain F: N.224 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain F: E.271, N.272 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain F: N.321, I.322, P.569, Q.570, T.571 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain F: F.332, N.333 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain F: N.606 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain F: N.647 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain F: N.699 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain F: A.696, E.1062, K.1063, N.1064 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain G: N.51 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain G: V.110, N.112, T.114, V.117, F.147 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain G: E.122, N.155, T.157 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain G: N.224 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain G: E.271, N.272 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain G: N.321, I.322, P.569, Q.570 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain G: N.333, F.364 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain G: N.606 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain G: N.647 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain G: N.699 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain A: Q.885 Chain G: A.696, E.1062, N.1064 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, Q. et al., Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein and potentially drive the genesis of Omicron variants. Nat Commun (2024)

Release Date

2024-08-21

Peptides

Spike glycoprotein,Fibritin,Expression Tag: AFG
Heavy chain of R1-32 Fab: BHJ
Light chain of R1-32 Fab: CIK
Light chain of H18 Fab: DLN
Heavy chain of H18 Fab: EMO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

F
A

G
B

B
G

H
H

J
N

C
I

I
L

K
O

D
D

L
F

N
K

E
E

M
J

O
M

Spike glycoprotein,Fibritin,Expression Tag

Heavy chain of R1-32 Fab

Light chain of R1-32 Fab

Light chain of H18 Fab

Heavy chain of H18 Fab

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