SMTL ID : 7so9.1

SARS-CoV-2 S B.1.617.2 delta variant + S2M11 + S2L20 Global Refinement

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

3 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 4 residues within 4Å: Chain A: G.337, N.341 Chain G: S.31 Chain H: F.104 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain A Hydrophobic interactions: H:F.104 Hydrogen bonds: A:N.341 NAG-FUC.2: 4 residues within 4Å: Chain F: G.337, N.341 Chain L: S.31 Chain M: F.104 2 PLIP interactions: 1 interactions with chain M, 1 interactions with chain F Hydrophobic interactions: M:F.104 Hydrogen bonds: F:N.341 NAG-FUC.3: 4 residues within 4Å: Chain B: S.31 Chain C: F.104 Chain K: G.337, N.341 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain K Hydrophobic interactions: C:F.104 Hydrogen bonds: K:N.341

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

NAG.4: 3 residues within 4Å: Chain A: N.61 Chain E: N.74, S.75 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.122, V.127, W.152 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.278, N.280 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain A: Q.115, E.132, N.163, T.165 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.329, Q.578 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.601 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: H.653, V.654, N.655 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.715, Q.924, Q.1069 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.799, S.801 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: A.704, E.1070, K.1071, N.1072 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: N.1096, T.1098, H.1099, F.1101 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.1132 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.614, T.616 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.707, G.1129 Chain K: D.794 Ligand excluded by PLIP NAG.18: 7 residues within 4Å: Chain A: T.114, Q.115, I.231, N.232 Chain D: R.30, Y.32 Chain E: R.103 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain F: N.61 Chain J: N.74, S.75 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain F: N.122, V.127, W.152 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain F: N.278, N.280 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain F: Q.115, E.132, N.163, T.165 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain F: N.329, Q.578 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain F: N.601 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain F: H.653, V.654, N.655 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain F: N.715, Q.924, Q.1069 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain F: N.799, S.801 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain F: A.704, E.1070, K.1071, N.1072 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain F: N.1096, T.1098, H.1099, F.1101 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain F: N.1132 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain F: N.614, T.616 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain A: D.794 Chain F: N.707, G.1129 Ligand excluded by PLIP NAG.33: 7 residues within 4Å: Chain F: T.114, Q.115, I.231, N.232 Chain I: R.30, Y.32 Chain J: R.103 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain K: N.61 Chain O: N.74, S.75 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain K: N.122, V.127, W.152 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain K: N.278, N.280 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain K: Q.115, E.132, N.163, T.165 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain K: N.329, Q.578 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain K: N.601 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain K: H.653, V.654, N.655 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain K: N.715, Q.924, Q.1069 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain K: N.799, S.801 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain K: A.704, E.1070, K.1071, N.1072 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain K: N.1096, T.1098, H.1099, F.1101 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain K: N.1132 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain K: N.614, T.616 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain F: D.794 Chain K: N.707, G.1129 Ligand excluded by PLIP NAG.48: 7 residues within 4Å: Chain K: T.114, Q.115, I.231, N.232 Chain N: R.30, Y.32 Chain O: R.103 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McCallum, M. et al., Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants. Science (2021)

Release Date

2021-11-17

Peptides

Spike glycoprotein: AFK
S2M11 Fab light chain: BGL
S2M11 Fab heavy chain: CHM
S2L20 Fab light chain: DIN
S2L20 Fab heavy chain: 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

S2M11 Fab heavy chain

S2L20 Fab light chain

S2L20 Fab heavy chain

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