SMTL ID : 7c2l.1

S protein of SARS-CoV-2 in complex bound with 4A8

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

6 x NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG.1: 3 residues within 4Å: Chain A: N.122, T.124, N.125 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.2: 2 residues within 4Å: Chain A: N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.10: 3 residues within 4Å: Chain B: N.122, T.124, N.125 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.11: 2 residues within 4Å: Chain B: N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.20: 3 residues within 4Å: Chain C: N.122, T.124, N.125 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.21: 2 residues within 4Å: Chain C: N.164, N.165 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.3: 3 residues within 4Å: Chain A: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: E.281, N.282 Chain C: K.558 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 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.6: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: N.1098, T.1100, 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.12: 3 residues within 4Å: Chain B: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain A: K.558 Chain B: E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain B: N.709, I.1130, G.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain B: A.706, S.711, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain B: N.1098, T.1100, H.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain C: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 3 residues within 4Å: Chain B: K.558 Chain C: E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, G.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 NAG-NAG.26: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 2 residues within 4Å: Chain C: A.706, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 3 residues within 4Å: Chain C: N.1098, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.30: 1 residues within 4Å: Chain A: N.17 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain A: N.149 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: N.331, Q.580, L.582 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain A: F.342, N.343, F.374 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain A: N.709 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain B: N.17 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain B: N.149 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain B: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain B: F.338, G.339, N.343 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.17 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain C: N.149 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain C: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chi, X. et al., A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2. Science (2020)

Release Date

2020-07-01

Peptides

Spike glycoprotein: ABC
heavy chain of 4A8: DFH
light chain of 4A8: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
I

H
J

E
L

G
M

I
N

Spike glycoprotein

heavy chain of 4A8

light chain of 4A8

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