SMTL ID : 7cyp.1

Complex of SARS-CoV-2 spike trimer with its neutralizing antibody HB27

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-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)

NAG-NAG.1: 3 residues within 4Å: Chain A: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: N.717, F.718, L.922, Q.926, Q.1071 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: 3 residues within 4Å: Chain A: N.1098, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: I.1132, V.1133, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain B: T.108, N.234, T.236 Chain C: R.457, E.465 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain B: N.717, F.718, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) 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: 3 residues within 4Å: Chain B: I.1132, V.1133, 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: 5 residues within 4Å: Chain C: N.717, L.922, N.925, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:N.925 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: 3 residues within 4Å: Chain C: I.1132, V.1133, N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.16: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.17: 7 residues within 4Å: Chain A: V.120, N.122, A.123, N.125, V.127, K.129, F.157 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain A: F.342, N.343, V.367, L.368, F.374 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.603 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 C: 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: 7 residues within 4Å: Chain B: V.120, N.122, A.123, N.125, V.127, K.129, F.157 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: 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: 5 residues within 4Å: Chain B: F.342, N.343, V.367, L.368, F.374 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: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain A: D.796 Chain B: N.709, G.1131 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain C: N.122, A.123, N.125, V.127 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: N.280, N.282 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: P.330, N.331, P.579, Q.580 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.603, T.604 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: H.655, V.656, N.657 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.709, I.1130 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain C: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, L. et al., Double lock of a potent human therapeutic monoclonal antibody against SARS-CoV-2. Natl Sci Rev (2021)

Release Date

2021-06-09

Peptides

SARS-CoV-2 Spike glycoprotein: ABC
Light chain of HB27: DFH
Heavy chain of HB27: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
F

H
H

E
E

G
G

I
I

SARS-CoV-2 Spike glycoprotein

Light chain of HB27

Heavy chain of HB27

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