SMTL ID : 7eh5.1

Cryo-EM structure of SARS-CoV-2 S-D614G variant in complex with neutralizing antibodies, RBD-chAb15 and RBD-chAb45

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

NAG-NAG.1: 2 residues within 4Å: Chain A: E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.331, P.579, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.616, T.618, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.709 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain A: S.704, A.706, E.1072, N.1074 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.706 NAG-NAG.8: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain J: E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain J: N.331, P.579, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain J: N.616, T.618, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain J: N.709 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain J: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain J: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain J: S.704, A.706, E.1072, N.1074 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:A.706 NAG-NAG.17: 4 residues within 4Å: Chain J: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 1 residues within 4Å: Chain J: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain K: E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain K: N.331, P.579, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain K: N.616, T.618, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 1 residues within 4Å: Chain K: N.709 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 3 residues within 4Å: Chain K: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain K: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain K: S.704, A.706, E.1072, N.1074 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:A.706 NAG-NAG.26: 4 residues within 4Å: Chain K: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 1 residues within 4Å: Chain K: N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.28: 3 residues within 4Å: Chain A: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain A: N.122, T.124 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain A: N.165 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: G.232, I.233, N.234 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: F.342, N.343 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain A: E.309, N.603 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain A: H.655, V.656, N.657 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain J: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain J: N.122, T.124 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain J: N.165 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain J: G.232, I.233, N.234 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain J: F.342, N.343 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain J: E.309, N.603 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain J: H.655, V.656, N.657 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain K: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain K: N.122, T.124 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain K: N.165 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain K: G.232, I.233, N.234 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain K: F.342, N.343 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain K: E.309, N.603 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain K: H.655, V.656, N.657 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, T.J. et al., Effect of SARS-CoV-2 B.1.1.7 mutations on spike protein structure and function. Nat.Struct.Mol.Biol. (2021)

Release Date

2021-09-01

Peptides

Spike glycoprotein: AJK
RBD-chAb45, heavy chain: BDE
RBD-chAb15, light chain: CNO
RBD-chAb15, heavy chain: FLM
RBD-chAb45, light chain: GHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

J
B

K
C

B
H

D
I

E
J

C
O

N
P

O
Q

F
F

L
D

M
E

G
L

H
M

I
N

Spike glycoprotein

RBD-chAb45, heavy chain

RBD-chAb15, light chain

RBD-chAb15, heavy chain

RBD-chAb45, light chain

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