SMTL ID : 7ly2.1

SARS-CoV-2 S/S2M11/S2M28 Global Refinement

Coordinates

PDB Format Compare

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: 6 residues within 4Å: Chain A: G.339, E.340, 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.4: 6 residues within 4Å: Chain F: G.339, E.340, 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.7: 6 residues within 4Å: Chain B: S.29, S.31 Chain C: F.104 Chain K: G.339, E.340, 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

6 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: 5 residues within 4Å: Chain A: N.717, L.922, N.925, Q.926, Q.1071 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.922, A:N.925 NAG-NAG.3: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain F: N.717, L.922, N.925, Q.926, Q.1071 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:L.922, F:N.925 NAG-NAG.6: 3 residues within 4Å: Chain F: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain K: N.717, L.922, N.925, Q.926, Q.1071 2 PLIP interactions: 2 interactions with chain K Hydrophobic interactions: K:L.922, K:N.925 NAG-NAG.9: 3 residues within 4Å: Chain K: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP)

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

NAG.10: 5 residues within 4Å: Chain A: C.15, N.17 Chain D: S.55, N.56, R.57 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: N.122, A.123, N.125, V.127 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.165 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.149, M.153 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.331, Q.580 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: 4 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: N.1098, T.1100, F.1103 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: I.1132, N.1134 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: T.108, N.234, T.236 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain F: C.15, N.17 Chain I: S.55, N.56, R.57 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain F: N.122, A.123, N.125, V.127 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain F: N.165 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain F: N.280, E.281, N.282 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain F: N.149, M.153 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain F: N.331, Q.580 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain F: N.603 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain F: N.616, Q.644 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain F: H.655, V.656, N.657 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain F: N.709, G.1131 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain F: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain F: N.1098, T.1100, F.1103 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain F: I.1132, N.1134 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain F: Y.28, N.61 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain F: T.108, N.234, T.236 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain K: C.15, N.17 Chain N: S.55, N.56, R.57 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain K: N.122, A.123, N.125, V.127 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain K: N.165 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain K: N.280, E.281, N.282 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain K: N.149, M.153 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain K: N.331, Q.580 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain K: N.603 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain K: N.616, Q.644 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain K: H.655, V.656, N.657 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain K: N.709, G.1131 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain K: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain K: N.1098, T.1100, F.1103 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain K: I.1132, N.1134 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain K: Y.28, N.61 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain K: T.108, N.234, T.236 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
S2M28 Fab Heavy Chain variable region: DIN
S2M28 Fab Light Chain variable region: EJO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
B

K
J

B
D

G
C

L
K

C
E

H
F

M
M

D
H

I
G

N
N

E
L

J
I

O
O

Spike glycoprotein

S2M11 Fab Light Chain variable region

S2M11 Fab Heavy Chain variable region

S2M28 Fab Heavy Chain variable region

S2M28 Fab Light Chain variable region

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