SMTL ID : 8csj.1

Cryo-EM structure of NTD-directed non-neutralizing antibody 4-33 in complex with prefusion SARS-CoV-2 spike glycoprotein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

5 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: N.109, T.111, N.112 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: C.2, N.4, N.124 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain D: N.109, A.110, T.111, N.112, V.114, V.158 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.158 NAG-NAG.5: 6 residues within 4Å: Chain E: N.109, A.110, T.111, N.112, V.114, V.158 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.158 NAG-NAG.6: 3 residues within 4Å: Chain E: C.2, N.4, N.124 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(2-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.4: 4 residues within 4Å: Chain D: K.545 Chain E: N.267, E.268, N.269 No protein-ligand interaction detected (PLIP)

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

NAG.7: 2 residues within 4Å: Chain A: N.318, Q.567 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: F.325, G.326, F.329, N.330 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.590 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: N.603, E.606 Chain D: I.831, R.834 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.644 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.696, G.1118 Chain D: D.783 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.151, N.152 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain A: H.133, N.135, N.136, S.138, M.140 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: E.268, N.269 Chain E: K.545 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.61 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain A: F.46, S.47, N.48, P.618, R.621 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: T.95, N.221, T.223 Chain E: S.446 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: K.449 Chain D: N.221, T.223 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain D: N.590 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain D: N.603 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain D: N.644 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain D: N.696 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain D: E.1059, N.1061 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain D: H.133, N.135, N.136, S.138, M.140 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: K.545 Chain D: N.269 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain D: N.61 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain D: F.46, N.48 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain D: C.2, N.4, N.124 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain E: N.318, P.566, Q.567 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain E: N.330 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain E: N.603, T.605 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain E: N.644 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain A: D.783 Chain E: N.696, G.1118 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain E: A.693, E.1059, N.1061 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain E: H.133, N.135, N.136, S.138 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain E: N.61 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain E: F.46, N.48 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain D: E.452 Chain E: T.95, N.221, T.223 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reddem, E.R. et al., Cryo-EM structure of NTD-directed non-neutralizing antibody 4-33 in complex with prefusion SARS-CoV-2 spike glycoprotein. To Be Published

Release Date

2023-05-17

Peptides

Spike glycoprotein: ADE
4-33 heavy chain: BFH
4-33 light chain: CGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

E
C

B
H

F
D

H
F

C
L

G
E

I
G

Spike glycoprotein

4-33 heavy chain

4-33 light chain