SMTL ID : 8zhk.1

SARS-CoV-2 spike trimer (6P) in complex with three H18 Fabs, head-to-head aggregate (C3 symmetry)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-6-mer

Ligands

24 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 B: N.707, L.912, Q.916, Q.1061 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.791, S.793, Q.794 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.1088, T.1090, H.1091, F.1093 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.1124 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: N.707, L.912, Q.916, Q.1061 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: N.791, S.793, Q.794 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: N.1088, T.1090, H.1091, F.1093 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain C: N.1124 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain J: N.707, L.912, Q.916, Q.1061 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain J: N.791, S.793, Q.794 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain J: N.1088, T.1090, H.1091, F.1093 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain J: N.1124 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain K: N.707, L.912, Q.916, Q.1061 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain K: N.791, S.793, Q.794 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain K: N.1088, T.1090, H.1091, F.1093 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain K: N.1124 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain L: N.707, L.912, N.915, Q.916, Q.1061 3 PLIP interactions: 3 interactions with chain L Hydrophobic interactions: L:N.915, L:Q.916 Hydrogen bonds: L:N.915 NAG-NAG.22: 3 residues within 4Å: Chain L: N.791, S.793, Q.794 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain L: N.1088, T.1090, H.1091, F.1093 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 1 residues within 4Å: Chain L: N.1124 No protein-ligand interaction detected (PLIP)

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

NAG.25: 2 residues within 4Å: Chain A: Y.18, N.51 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: N.112, T.114, V.117, F.147 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain A: E.122, N.155, T.157 Chain C: R.345 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain A: N.224 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: E.271, N.272 Chain C: K.548 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain A: N.321, I.322, Q.570 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain A: F.332, N.333 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain A: N.606 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain A: N.647 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain A: N.699 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain A: A.696, E.1062, K.1063, N.1064 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.51 Ligand excluded by PLIP NAG.37: 5 residues within 4Å: Chain B: V.110, N.112, T.114, V.117, F.147 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain A: R.345 Chain B: E.122, N.155, T.157 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: N.224, T.226 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: E.271, N.272 Ligand excluded by PLIP NAG.41: 5 residues within 4Å: Chain B: N.321, I.322, P.569, Q.570, L.572 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: N.333, F.364 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain B: N.606 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain B: N.647 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain B: N.699 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain B: A.696, E.1062, N.1064 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: Y.18, N.51 Ligand excluded by PLIP NAG.48: 5 residues within 4Å: Chain C: V.110, N.112, T.114, V.117, F.147 Ligand excluded by PLIP NAG.49: 5 residues within 4Å: Chain B: R.345, R.456 Chain C: Q.105, N.155, T.157 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain C: N.224 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain B: K.548 Chain C: E.271, N.272 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain C: N.321, I.322, P.569, Q.570 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain C: N.333 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.606 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain C: H.645, N.647 Ligand excluded by PLIP NAG.56: 1 residues within 4Å: Chain C: N.699 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain C: N.1064 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain J: Y.18, N.51 Ligand excluded by PLIP NAG.59: 4 residues within 4Å: Chain J: N.112, T.114, V.117, F.147 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain J: E.122, N.155, T.157 Ligand excluded by PLIP NAG.61: 1 residues within 4Å: Chain J: N.224 Ligand excluded by PLIP NAG.62: 3 residues within 4Å: Chain J: E.271, N.272 Chain L: K.548 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain J: N.321, I.322, Q.570 Ligand excluded by PLIP NAG.64: 2 residues within 4Å: Chain J: F.332, N.333 Ligand excluded by PLIP NAG.65: 1 residues within 4Å: Chain J: N.606 Ligand excluded by PLIP NAG.66: 1 residues within 4Å: Chain J: N.647 Ligand excluded by PLIP NAG.67: 1 residues within 4Å: Chain J: N.699 Ligand excluded by PLIP NAG.68: 4 residues within 4Å: Chain J: A.696, E.1062, K.1063, N.1064 Ligand excluded by PLIP NAG.69: 1 residues within 4Å: Chain K: N.51 Ligand excluded by PLIP NAG.70: 5 residues within 4Å: Chain K: V.110, N.112, T.114, V.117, F.147 Ligand excluded by PLIP NAG.71: 3 residues within 4Å: Chain K: E.122, N.155, T.157 Ligand excluded by PLIP NAG.72: 1 residues within 4Å: Chain K: N.224 Ligand excluded by PLIP NAG.73: 2 residues within 4Å: Chain K: E.271, N.272 Ligand excluded by PLIP NAG.74: 3 residues within 4Å: Chain K: N.321, Q.570, T.571 Ligand excluded by PLIP NAG.75: 2 residues within 4Å: Chain K: N.333, F.364 Ligand excluded by PLIP NAG.76: 1 residues within 4Å: Chain K: N.606 Ligand excluded by PLIP NAG.77: 1 residues within 4Å: Chain K: N.647 Ligand excluded by PLIP NAG.78: 1 residues within 4Å: Chain K: N.699 Ligand excluded by PLIP NAG.79: 3 residues within 4Å: Chain K: A.696, E.1062, N.1064 Ligand excluded by PLIP NAG.80: 1 residues within 4Å: Chain L: N.51 Ligand excluded by PLIP NAG.81: 6 residues within 4Å: Chain L: V.110, N.112, T.114, N.115, V.117, F.147 Ligand excluded by PLIP NAG.82: 3 residues within 4Å: Chain L: Q.105, N.155, T.157 Ligand excluded by PLIP NAG.83: 1 residues within 4Å: Chain L: N.224 Ligand excluded by PLIP NAG.84: 3 residues within 4Å: Chain K: K.548 Chain L: E.271, N.272 Ligand excluded by PLIP NAG.85: 2 residues within 4Å: Chain L: N.321, I.322 Ligand excluded by PLIP NAG.86: 1 residues within 4Å: Chain L: N.333 Ligand excluded by PLIP NAG.87: 1 residues within 4Å: Chain L: N.606 Ligand excluded by PLIP NAG.88: 2 residues within 4Å: Chain L: H.645, N.647 Ligand excluded by PLIP NAG.89: 1 residues within 4Å: Chain L: N.699 Ligand excluded by PLIP NAG.90: 1 residues within 4Å: Chain L: 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: ABCJKL
Light chain of H18 Fab: DFHMOQ
Heavy chain of H18 Fab: EGINPR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

J
G

K
H

L
I

D
D

F
F

H
K

M
L

O
O

Q
Q

E
E

G
J

I
M

N
N

P
P

R
R

Spike glycoprotein,Fibritin,Expression Tag

Light chain of H18 Fab

Heavy chain of H18 Fab

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