SMTL ID : 7ra8.1

SARS-CoV-2 S glycoprotein in complex with S2X259 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

12 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: 3 residues within 4Å: Chain A: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain D: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain D: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain D: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain D: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain G: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain G: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain G: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain G: N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.13: 2 residues within 4Å: Chain A: F.59, N.61 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: G.199, G.232, N.234 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.280, N.282 Chain D: K.558 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.616, Q.644 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: H.655, V.656, N.657 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: F.342, N.343 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: N.331, P.579, Q.580, L.582 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain D: F.59, N.61 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain D: G.199, G.232, N.234 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain D: N.280, N.282 Chain G: K.558 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain D: N.603 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain D: N.616, Q.644 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain D: H.655, V.656, N.657 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain D: N.709, G.1131 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain D: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain D: F.342, N.343 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain D: N.331, P.579, Q.580, L.582 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain G: F.59, N.61 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain G: G.199, G.232, N.234 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: K.558 Chain G: N.280, N.282 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain G: N.603 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain G: N.616, Q.644 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain G: H.655, V.656, N.657 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain G: N.709, G.1131 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain G: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain G: F.342, N.343 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain G: N.331, P.579, Q.580, L.582 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tortorici, M.A. et al., Broad sarbecovirus neutralization by a human monoclonal antibody. Nature (2021)

Release Date

2021-08-04

Peptides

Spike glycoprotein: ADG
Heavy chain Fab S2X259 Fab variable domain: BEH
Light chain Fab S2X259 Fab variable domain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
E

B
H

E
C

H
F

C
L

F
D

I
G

Spike glycoprotein

Heavy chain Fab S2X259 Fab variable domain

Light chain Fab S2X259 Fab variable domain

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