SMTL ID : 8hp9.1

Cryo-EM structure of SARS-CoV-2 Omicron BA.2 S-trimer in complex with fab L4.65 and L5.34

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: D.323, N.327, V.351, N.354, F.355 Ligand excluded by PLIP NAG.2: 2 residues within 4Å: Chain A: Y.12, N.45 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: N.315, Q.564 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain A: N.600 Chain K: K.819 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain A: N.693 Chain K: Y.780 Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain A: N.701, L.906, Q.910, Q.1055 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: N.785, S.787, Q.788 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: A.690, E.1056, N.1058 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: N.1082, T.1084, H.1085, F.1087 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.1118 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: Y.780 Chain F: N.693 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain F: N.327, N.354, F.355 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain F: N.106, T.108, N.109, V.111 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain F: N.264, E.265, N.266 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain F: N.315, Q.564, L.566 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain F: N.600, Q.628 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain F: N.701, L.906, Q.910, Q.1055 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain F: N.785, S.787, Q.788 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain F: A.690, E.1056, N.1058 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain F: N.1082, T.1084, H.1085, F.1087 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain F: N.1118 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain K: D.323, N.327, N.354 Ligand excluded by PLIP NAG.23: 5 residues within 4Å: Chain K: N.106, T.108, N.109, V.111, E.138 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain K: Y.12, N.45 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain K: N.315, Q.564 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain F: I.818, K.819 Chain K: N.600, T.602 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain F: Y.780 Chain K: N.693 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain K: N.701, Q.910, Q.1055 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain K: N.785, S.787, Q.788 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain K: A.690, E.1056, N.1058 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain K: N.1082, T.1084, F.1087 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain K: N.1118 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, S. et al., Dosing interval regimen shapes potency and breadth of antibody repertoire after vaccination of SARS-CoV-2 RBD protein subunit vaccine. Cell Discov (2023)

Release Date

2024-01-31

Peptides

Spike protein S2': AFK
fab L4.65: BHM
fab L4.65: CGL
fab L5.34: DIN
fab L5.34: EJO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
B

K
C

B
L

H
Q

M
J

C
H

G
P

L
I

D
M

I
E

N
K

E
N

J
F

O
O

Spike protein S2'

fab L4.65

fab L4.65

fab L5.34

fab L5.34

Related Entries With Identical Sequence