SMTL ID : 7kkl.1

SARS-CoV-2 Spike in complex with neutralizing nanobody mNb6

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

18 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: 4 residues within 4Å: Chain A: T.108, T.109, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 7 residues within 4Å: Chain A: T.716, N.717, T.719, L.922, N.925, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.3: 4 residues within 4Å: Chain A: N.801, S.803, Q.804, Q.935 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: N.1098, G.1099, T.1100, H.1101, F.1103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.1101 NAG-NAG.5: 3 residues within 4Å: Chain A: D.1084, G.1085, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 8 residues within 4Å: Chain A: F.338, G.339, F.342, N.343, V.367, L.368, F.374 Chain F: E.44 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.367 NAG-NAG.7: 4 residues within 4Å: Chain C: T.108, T.109, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 7 residues within 4Å: Chain C: T.716, N.717, T.719, L.922, N.925, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 NAG-NAG.9: 4 residues within 4Å: Chain C: N.801, S.803, Q.804, Q.935 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain C: N.1098, G.1099, T.1100, H.1101, F.1103 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.1101 NAG-NAG.11: 3 residues within 4Å: Chain C: D.1084, G.1085, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 7 residues within 4Å: Chain B: E.44 Chain C: F.338, G.339, F.342, N.343, V.367, L.368 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.367 NAG-NAG.13: 4 residues within 4Å: Chain E: T.108, T.109, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 7 residues within 4Å: Chain E: T.716, N.717, T.719, L.922, N.925, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:L.922 NAG-NAG.15: 4 residues within 4Å: Chain E: N.801, S.803, Q.804, Q.935 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 5 residues within 4Å: Chain E: N.1098, G.1099, T.1100, H.1101, F.1103 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:H.1101 NAG-NAG.17: 3 residues within 4Å: Chain E: D.1084, G.1085, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 7 residues within 4Å: Chain D: E.44 Chain E: F.338, G.339, F.342, N.343, V.367, L.368 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.367

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

NAG.19: 4 residues within 4Å: Chain A: Y.28, F.59, S.60, N.61 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: N.280, E.281, N.282, T.286 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: V.615, N.616, T.618, Q.644 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: H.655, V.656, N.657, N.658 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.25: 6 residues within 4Å: Chain A: A.706, A.713, E.1072, K.1073, N.1074 Chain C: Q.895 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: E.132, N.165 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain A: N.331, P.579, Q.580, L.582 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain C: Y.28, F.59, S.60, N.61 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain C: N.280, E.281, N.282, T.286 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain C: V.615, N.616, T.618, Q.644 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain C: H.655, V.656, N.657, N.658 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.34: 6 residues within 4Å: Chain C: A.706, A.713, E.1072, K.1073, N.1074 Chain E: Q.895 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: E.132, N.165 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: N.331, P.579, Q.580, L.582 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain E: Y.28, F.59, S.60, N.61 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain E: N.280, E.281, N.282, T.286 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain E: N.603 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain E: V.615, N.616, T.618, Q.644 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain E: H.655, V.656, N.657, N.658 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain E: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.43: 6 residues within 4Å: Chain A: Q.895 Chain E: A.706, A.713, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain E: E.132, N.165 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain E: N.331, P.579, Q.580, L.582 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schoof, M. et al., An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike. Science (2020)

Release Date

2020-11-11

Peptides

Spike glycoprotein: ACE
Synthetic nanobody mNb6: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
D

B
B

D
E

F
F

Spike glycoprotein

Synthetic nanobody mNb6

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