SMTL ID : 8gjm.1

17b10 fab in complex with full-length SARS-CoV-2 Spike G614 trimer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-mer

Ligands

24 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: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: N.122, T.124, N.125, V.127, F.157 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.331, P.579, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.616, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 7 residues within 4Å: Chain A: N.717, F.718, T.719, L.922, N.925, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.926 NAG-NAG.6: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain A: F.338, G.339, F.342, N.343, V.367 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 7 residues within 4Å: Chain B: N.122, A.123, T.124, N.125, E.154, E.169, V.171 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.171 Hydrogen bonds: B:N.125 NAG-NAG.13: 3 residues within 4Å: Chain B: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain B: N.616, T.618 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 6 residues within 4Å: Chain B: N.717, F.718, L.922, N.925, Q.926, Q.1071 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.922, B:N.925, B:Q.926 Hydrogen bonds: B:N.925 NAG-NAG.16: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain B: F.338, G.339, F.342, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain B: E.132, N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain C: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 6 residues within 4Å: Chain C: N.122, A.123, T.124, N.125, E.154, V.171 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.171 NAG-NAG.24: 7 residues within 4Å: Chain B: R.457, K.458, K.462, E.465 Chain C: T.108, N.234, T.236 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.458 NAG-NAG.25: 3 residues within 4Å: Chain C: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 6 residues within 4Å: Chain C: N.717, F.718, L.922, N.925, Q.926, Q.1071 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.922, C:Q.926 Hydrogen bonds: C:N.925 NAG-NAG.27: 2 residues within 4Å: Chain C: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 3 residues within 4Å: Chain C: F.338, G.339, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 3 residues within 4Å: Chain B: Y.351, I.468 Chain C: N.165 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.7: 2 residues within 4Å: Chain A: E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.17: 4 residues within 4Å: Chain B: A.706, E.1072, K.1073, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.28: 2 residues within 4Å: Chain C: E.1072, N.1074 No protein-ligand interaction detected (PLIP)

5 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.8: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.9: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.18: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.19: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.29: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP)

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

NAG.33: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain A: Y.144, K.147, N.148, N.149 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain A: T.108, N.234, T.236 Chain C: E.465 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain A: E.281, N.282 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain A: N.709 Chain B: I.794, D.796 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain A: N.1158 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain A: E.132, N.165 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain B: Y.28, N.30, F.59, N.61 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain B: Y.144, K.147, N.148, N.149 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain B: N.234 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain B: H.655, V.656, N.657 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain B: N.709, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain A: K.1157 Chain B: N.1158 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain C: Y.144, K.147, N.148, N.149 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain C: P.330, N.331, P.579, Q.580 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain C: N.616, Q.644 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain C: H.655, V.656, N.657 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, N.710 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain B: K.1157 Chain C: Y.1155, N.1158 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kwon, H.J. et al., Distinct in vitro and in vivo neutralization profiles of monoclonal antibodies elicited by the receptor binding domain of the ancestral SARS-CoV-2. J Med Virol (2023)

Release Date

2023-04-05

Peptides

Spike glycoprotein: ABC
Heavy chain of 17B10 fab: D
Light chain of 17B10 fab: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Spike glycoprotein

Heavy chain of 17B10 fab

Light chain of 17B10 fab

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