SMTL ID : 7ly2.1

SARS-CoV-2 S/S2M11/S2M28 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: 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

Related Entries With Identical Sequence