SMTL ID : 7cac.1

SARS-CoV-2 S trimer with one RBD in the open state and complexed with one H014 Fab.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-mer

Ligands

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

NAG-NAG.1: 5 residues within 4Å: Chain A: T.108, N.234, T.236 Chain C: R.457, E.465 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.457 NAG-NAG.2: 3 residues within 4Å: Chain A: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: I.1132, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain A: R.457, E.465 Chain B: T.108, N.234, T.236 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.457, A:R.457 NAG-NAG.7: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG.8: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: N.1098, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain B: I.1132, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain C: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain C: I.1132, N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.16: 1 residues within 4Å: Chain A: N.61 Ligand excluded by PLIP NAG.17: 7 residues within 4Å: Chain A: N.122, A.123, N.125, V.127, E.154, S.155, F.157 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: E.281, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.20: 7 residues within 4Å: Chain A: F.338, G.339, N.343, V.367, L.368, N.370, S.371 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.603, T.604 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: H.655, V.656, N.657 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: N.709, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.122, N.125, V.127 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain A: K.558 Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.30: 7 residues within 4Å: Chain B: F.338, G.339, F.342, N.343, L.368, N.370, S.371 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: H.655, V.656, N.657 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: N.709, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.61 Ligand excluded by PLIP NAG.37: 7 residues within 4Å: Chain C: N.122, A.123, N.125, V.127, E.154, S.155, F.157 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: K.558 Chain C: E.281, N.282 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.40: 7 residues within 4Å: Chain C: F.338, G.339, N.343, V.367, L.368, N.370, S.371 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.603, T.604 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: H.655, V.656, N.657 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lv, Z. et al., Structural basis for neutralization of SARS-CoV-2 and SARS-CoV by a potent therapeutic antibody. Science (2020)

Release Date

2021-02-24

Peptides

Spike glycoprotein: ABC
Light chain of H014 Fab: D
Heavy chain of H014 Fab: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Spike glycoprotein

Light chain of H014 Fab

Heavy chain of H014 Fab

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