SMTL ID : 7mkl.1

SARS-CoV-2 Spike in complex with neutralizing Fab SARS2-38 (three down conformation)

Coordinates

PDB Format

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)

NAG-NAG.1: 4 residues within 4Å: Chain A: Q.89, N.208, T.210, R.211 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.691, L.896, Q.1045 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.775, S.777 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.1072, T.1074, H.1075, F.1077 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.1075 NAG-NAG.5: 2 residues within 4Å: Chain A: I.1106, N.1108 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain B: T.82, T.88, N.208, T.210, R.211 Chain C: R.440 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.211 NAG-NAG.7: 3 residues within 4Å: Chain B: N.691, L.896, Q.1045 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.775, S.777, Q.778 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: N.1072, T.1074, H.1075, F.1077 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain B: N.1108 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain A: E.439 Chain C: T.82, N.208, T.210, R.211 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain C: N.691, L.896 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.896 NAG-NAG.13: 2 residues within 4Å: Chain C: N.775, S.777 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain C: N.1072, T.1074, H.1075, F.1077 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain C: I.1106, N.1108 No protein-ligand interaction detected (PLIP)

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

NAG.16: 3 residues within 4Å: Chain A: F.33, S.34, N.35 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain A: N.96, A.97, N.99, V.101, V.145 Ligand excluded by PLIP NAG.18: 8 residues within 4Å: Chain A: S.86, K.87, T.88, Q.89, E.106, N.139 Chain B: A.326, R.440 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: N.254, N.256, T.258 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: N.305, Q.554 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.317, S.345 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.577 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.590, Q.618 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: H.629, V.630, N.631 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: N.683, N.684, G.1105 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: A.680, N.1048 Chain C: Q.869 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: A.1, Y.2, N.35 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: R.76, N.96, N.99 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain B: S.86, K.87, E.106, N.139 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.256 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.305, Q.554 Ligand excluded by PLIP NAG.32: 6 residues within 4Å: Chain B: F.312, G.313, F.316, N.317, V.341, L.342 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.577 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain B: V.589, N.590, Q.618, T.619, G.622 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain B: N.631 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.683, G.1105 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: A.680, N.1048 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: A.1, Y.2, N.35 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: V.94, N.96, N.99, V.101 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: E.106, N.139 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.254, N.256 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.305, Q.554 Ligand excluded by PLIP NAG.43: 6 residues within 4Å: Chain C: F.312, G.313, F.316, N.317, V.341, L.342 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.577 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: V.589, N.590 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: H.629, N.631 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.683 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain B: Q.869 Chain C: A.680, N.1048 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

VanBlargan, L.A. et al., A potently neutralizing SARS-CoV-2 antibody inhibits variants of concern by utilizing unique binding residues in a highly conserved epitope. Immunity (2021)

Release Date

2021-05-12

Peptides

Spike glycoprotein: ABC
SARS2-38 Fv heavy chain: D
SARS2-38 Fv light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
L

Spike glycoprotein

SARS2-38 Fv heavy chain

SARS2-38 Fv light chain

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