SMTL ID : 7n8h.1

SARS-CoV-2 S (B.1.429 / epsilon variant) + S2M11 + S2L20 Global Refinement

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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.1: 6 residues within 4Å: Chain A: G.339, N.343 Chain L: S.29, S.31, Y.32 Chain M: F.104 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain M, 1 interactions with chain L Water bridges: A:G.339 Hydrophobic interactions: M:F.104 Hydrogen bonds: L:Y.32 NAG-NAG-FUC.4: 6 residues within 4Å: Chain B: S.29, S.31, Y.32 Chain C: F.104 Chain F: G.339, N.343 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: C:F.104 Water bridges: F:G.339 Hydrogen bonds: B:Y.32 NAG-NAG-FUC.7: 6 residues within 4Å: Chain G: S.29, S.31, Y.32 Chain H: F.104 Chain K: G.339, N.343 3 PLIP interactions: 1 interactions with chain K, 1 interactions with chain H, 1 interactions with chain G Water bridges: K:G.339 Hydrophobic interactions: H:F.104 Hydrogen bonds: G:Y.32

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: 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.5: 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.6: 3 residues within 4Å: Chain F: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 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.9: 3 residues within 4Å: Chain K: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP)

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

NAG.10: 2 residues within 4Å: Chain A: N.122, A.123 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: F.59, N.61 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.234 Chain E: R.103, Y.104 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.165 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: E.281, N.282 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain F: N.122, A.123 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain F: F.59, N.61 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain F: N.234 Chain J: R.103, Y.104 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain F: N.165 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain F: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain F: N.603 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain F: H.655, N.657 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain F: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain F: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain F: N.1134 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain F: N.616 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain F: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain F: E.281, N.282 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain K: N.122, A.123 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain K: F.59, N.61 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain K: N.234 Chain O: R.103, Y.104 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain K: N.165 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain K: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain K: N.603 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain K: H.655, N.657 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain K: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain K: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain K: N.1134 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain K: N.616 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain K: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain K: E.281, N.282 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McCallum, M. et al., SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern. Science (2021)

Release Date

2021-07-14

Peptides

Spike glycoprotein: AFK
S2M11 Fab Light Chain variable region: BGL
S2M11 Fab Heavy Chain variable region: CHM
S2L20 Fab Light Chain variable region: DIN
S2L20 Fab Heavy Chain variable region: EJO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
F

K
K

B
D

G
G

L
L

C
E

H
H

M
M

D
B

I
I

N
N

E
C

J
J

O
O

Spike glycoprotein

S2M11 Fab Light Chain variable region

S2M11 Fab Heavy Chain variable region

S2L20 Fab Light Chain variable region

S2L20 Fab Heavy Chain variable region

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