SMTL ID : 7lxz.1

SARS-CoV-2 S/S2M11/S2L28 Global Refinement

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

3 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.1: 5 residues within 4Å: Chain A: G.339, N.343 Chain G: S.29, S.31 Chain H: F.104 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:F.104 Hydrogen bonds: G:S.29 NAG-NAG-BMA-FUC.6: 5 residues within 4Å: Chain F: G.339, N.343 Chain L: S.29, S.31 Chain M: F.104 2 PLIP interactions: 1 interactions with chain M, 1 interactions with chain L Hydrophobic interactions: M:F.104 Hydrogen bonds: L:S.29 NAG-NAG-BMA-FUC.11: 5 residues within 4Å: Chain B: S.29, S.31 Chain C: F.104 Chain K: G.339, N.343 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.104 Hydrogen bonds: B:S.29

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

NAG-NAG.2: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.3: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: H.146, N.149, S.151 Chain D: L.106 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.106 NAG-NAG.7: 4 residues within 4Å: Chain F: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:L.922 NAG-NAG.8: 3 residues within 4Å: Chain F: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain F: H.146, N.149, S.151 Chain I: L.106 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:L.106 NAG-NAG.12: 4 residues within 4Å: Chain K: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:L.922 NAG-NAG.13: 3 residues within 4Å: Chain K: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain K: H.146, N.149, S.151 Chain N: L.106 1 PLIP interactions: 1 interactions with chain N Hydrophobic interactions: N:L.106

3 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.5: 4 residues within 4Å: Chain A: C.15, V.16, N.17, N.137 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.137 NAG-NAG-FUC.10: 4 residues within 4Å: Chain F: C.15, V.16, N.17, N.137 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.137 NAG-NAG-FUC.15: 4 residues within 4Å: Chain K: C.15, V.16, N.17, N.137 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:N.137

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

NAG.16: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.616, Q.644 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: N.1098, T.1100, F.1103 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: I.1132, N.1134 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain A: N.122, A.123, T.124, V.127, E.154 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.280, N.282 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: T.108, N.234, T.236 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: N.164, N.165 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain F: N.331, Q.580 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain F: N.603 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain F: N.616, Q.644 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain F: H.655, N.657 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain F: N.709, G.1131 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain F: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain F: N.1098, T.1100, F.1103 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain F: I.1132, N.1134 Ligand excluded by PLIP NAG.37: 5 residues within 4Å: Chain F: N.122, A.123, T.124, V.127, E.154 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain F: N.280, N.282 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain F: T.108, N.234, T.236 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain F: N.164, N.165 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain F: Y.28, N.61 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain K: N.331, Q.580 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain K: N.603 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain K: N.616, Q.644 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain K: H.655, N.657 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain K: N.709, G.1131 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain K: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain K: N.1098, T.1100, F.1103 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain K: I.1132, N.1134 Ligand excluded by PLIP NAG.50: 5 residues within 4Å: Chain K: N.122, A.123, T.124, V.127, E.154 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain K: N.280, N.282 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain K: T.108, N.234, T.236 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain K: N.164, N.165 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain K: Y.28, N.61 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McCallum, M. et al., N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2. Cell (2021)

Release Date

2021-04-14

Peptides

Spike glycoprotein: AFK
S2M11 Fab Light Chain variable region: BGL
S2M11 Fab Heavy Chain variable region: CHM
S2L28 Fab Heavy Chain variable region: DIN
S2L28 Fab Light Chain variable region: EJO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
B

K
K

B
D

G
C

L
L

C
E

H
F

M
M

D
H

I
G

N
N

E
J

J
I

O
O

Spike glycoprotein

S2M11 Fab Light Chain variable region

S2M11 Fab Heavy Chain variable region

S2L28 Fab Heavy Chain variable region

S2L28 Fab Light Chain variable region

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