SMTL ID : 8dxs.1

Cryo-EM structure of RBD-directed neutralizing antibody P2B4 in complex with prefusion SARS-CoV-2 spike glycoprotein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.2: 4 residues within 4Å: Chain A: Y.28, T.29, N.30, N.61 Ligand excluded by PLIP NAG.3: 3 residues within 4Å: Chain A: N.122, N.125, V.127 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain A: E.132, N.165 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: G.232, I.233, N.234 Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain A: E.281, N.282 Chain C: K.557, K.558 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.331, I.332 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.9: 5 residues within 4Å: Chain A: T.307, V.308, G.601, T.602, N.603 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: V.656, N.657, N.658 Ligand excluded by PLIP NAG.12: 5 residues within 4Å: Chain A: N.709 Chain B: D.796, F.797, G.798, G.799 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.717, L.922, Q.1071 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: K.795, N.801, S.803 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: I.1132, V.1133, N.1134 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: K.558 Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.19: 6 residues within 4Å: Chain B: F.329, P.330, N.331, I.332, N.544, P.579 Ligand excluded by PLIP NAG.20: 9 residues within 4Å: Chain B: F.338, G.339, N.343, V.367, L.368, Y.369, N.370, S.371, A.372 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: N.603, T.604 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.616, Q.644 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: H.655, V.656, N.657 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: N.709, N.710 Chain C: I.794, D.796 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: N.717, L.922, Q.926 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: K.795, N.801, S.803, Q.804 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain B: A.713, E.1072, K.1073, N.1074 Chain C: Q.895 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: I.1132, V.1133, N.1134 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: N.122, T.124, N.125 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: G.232, I.233, N.234 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain C: N.331, I.332, P.579, Q.580 Ligand excluded by PLIP NAG.35: 8 residues within 4Å: Chain C: F.338, G.339, F.342, N.343, V.367, L.368, N.370, S.371 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.603, T.604 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: H.655, V.656, N.657 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, I.1130 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain C: T.716, N.717, N.919, L.922, Q.1071 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.801 Ligand excluded by PLIP NAG.42: 6 residues within 4Å: Chain A: A.893, Q.895 Chain C: A.706, A.713, E.1072, N.1074 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: I.1132, V.1133, N.1134 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luo, M. et al., Structural insights into broadly neutralizing antibodies elicited by hybrid immunity against SARS-CoV-2. Emerg Microbes Infect (2023)

Release Date

2022-12-07

Peptides

Spike glycoprotein: ABC
P2B4 Heavy chain: DFH
P2B4 Light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
F

H
G

E
L

G
I

I
J

Spike glycoprotein

P2B4 Heavy chain

P2B4 Light chain

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