SMTL ID : 7jv4.1

SARS-CoV-2 spike in complex with the S2H13 neutralizing antibody (one RBD open)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

11 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: 4 residues within 4Å: Chain A: N.736, T.738, L.941, Q.945 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.941 NAG-NAG.2: 3 residues within 4Å: Chain A: N.820, S.822, Q.823 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1117, T.1119, H.1120, F.1122 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: I.1151, N.1153 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.820, S.822, Q.823 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.1117, T.1119, H.1120, F.1122 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: I.1151, V.1152, N.1153 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: N.736, L.941, Q.945 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.941 NAG-NAG.9: 2 residues within 4Å: Chain C: N.820, S.822 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain C: N.1117, T.1119, H.1120, F.1122 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain C: I.1151, N.1153 No protein-ligand interaction detected (PLIP)

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

NAG.12: 3 residues within 4Å: Chain A: Y.47, T.48, N.80 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: N.141, A.142, T.143, N.144 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.253, T.255 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.299, E.300, N.301 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.350, Q.599 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain A: F.357, G.358, N.362, V.386, L.387 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.622 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.635, Q.663 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: H.674, N.676 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.728, G.1150 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: A.725, E.1091, K.1092, N.1093 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain B: Y.47, T.48, N.49, N.80 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.141, A.142 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: T.127, N.253, T.255 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: K.577 Chain B: N.299, N.301 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.350, P.598, Q.599 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: F.361, N.362 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.622 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.635, T.637 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: H.674, N.676 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.728, G.1150 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain B: T.735, N.736, N.938, L.941 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain B: A.725, E.1091, K.1092, N.1093 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain B: N.184 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: Y.47, T.48, N.49, N.80 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.141, A.142, T.143 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.253 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.299, N.301 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.350, I.351 Ligand excluded by PLIP NAG.41: 5 residues within 4Å: Chain C: F.357, G.358, N.362, V.386, L.387 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.622 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.635 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: H.674, N.676 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: N.728, I.1149, G.1150 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain C: A.725, E.1091, K.1092, N.1093 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.184 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Piccoli, L. et al., Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology. Cell (2020)

Release Date

2020-10-14

Peptides

Spike glycoprotein: ABC
S2H13 Fab heavy chain: DFH
S2H13 Fab light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
F

H
D

E
L

G
G

I
E

Spike glycoprotein

S2H13 Fab heavy chain

S2H13 Fab light chain

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