SMTL ID : 8vye.1

SARS-CoV-2 S (C.37 Lambda variant) plus S309, S2L20, and S2X303 Fabs

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-3-3-3-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: P.323, N.324, P.572, Q.573 Ligand excluded by PLIP NAG.2: 1 residues within 4Å: Chain A: N.596 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: H.648, N.650 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: A.699, E.1065, N.1067 Ligand excluded by PLIP NAG.5: 4 residues within 4Å: Chain A: N.1091, T.1093, H.1094, F.1096 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain A: N.1127 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.609, T.611 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: N.702, I.1123, G.1124 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.794, S.796, Q.797 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: N.710, Q.919, Q.1064 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: G.332, N.336 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.273, N.275 Ligand excluded by PLIP NAG.13: 6 residues within 4Å: Chain A: N.122, T.124, N.125, V.127, V.171 Chain F: G.32 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.165 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.149 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.17 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.234 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: R.158, N.246, W.251 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: F.59, N.61 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain H: P.323, N.324, P.572, Q.573 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain H: N.596 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain H: H.648, N.650 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain H: A.699, E.1065, N.1067 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain H: N.1091, T.1093, H.1094, F.1096 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain H: N.1127 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain H: N.609, T.611 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain H: N.702, I.1123, G.1124 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain H: N.794, S.796, Q.797 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain H: N.710, Q.919, Q.1064 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain H: G.332, N.336 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain H: N.273, E.274, N.275 Ligand excluded by PLIP NAG.32: 6 residues within 4Å: Chain H: N.122, T.124, N.125, V.127, V.171 Chain M: G.32 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain H: N.165 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain H: N.149 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain H: N.17 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain H: N.234 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain H: R.158, N.246, W.251 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain H: F.59, N.61 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain O: P.323, N.324, P.572, Q.573 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain O: N.596 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain O: H.648, N.650 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain O: A.699, E.1065, N.1067 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain O: N.1091, T.1093, H.1094, F.1096 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain O: N.1127 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain O: N.609, T.611 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain O: N.702, I.1123, G.1124 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain O: N.794, S.796, Q.797 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain O: N.710, Q.919, Q.1064 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain O: G.332, N.336 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain O: N.273, E.274, N.275 Ligand excluded by PLIP NAG.51: 6 residues within 4Å: Chain O: N.122, T.124, N.125, V.127, V.171 Chain T: G.32 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain O: N.165 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain O: N.149 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain O: N.17 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain O: N.234 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain O: R.158, N.246, W.251 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain O: F.59, N.61 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Magaret, C.A. et al., Quantifying how single dose Ad26.COV2.S vaccine efficacy depends on Spike sequence features. Nat Commun (2024)

Release Date

2024-03-27

Peptides

Spike glycoprotein: AHO
S2L20 Heavy Chain: BIP
S2L20 Light Chain: CJQ
S309 Heavy Chain: DKR
S309 Light Chain: ELS
S2X303 Heavy Chain: FMT
S2X303 Light Chain: GNU

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

H
E

O
O

B
B

I
F

P
P

C
C

J
G

Q
Q

D
A

K
I

R
R

E
D

L
J

S
S

F
H

M
M

T
T

G
L

N
N

U
U

Spike glycoprotein

S2L20 Heavy Chain

S2L20 Light Chain

S309 Heavy Chain

S309 Light Chain

S2X303 Heavy Chain

S2X303 Light Chain

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