SMTL ID : 9lyo.1

Alpha SARS-CoV-2 spike protein in complex with REGN10987 Fab homologue.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

31 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 D: F.341, G.342, F.345, N.346 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain C: V.124, N.125, N.126, T.128, V.131, E.157 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain C: E.284, N.285 Chain E: K.561 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain C: N.334, P.582, Q.583, T.584 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain C: N.619, T.621 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain C: N.712 Chain D: D.799 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain C: N.720, L.925, Q.929, Q.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain C: N.804, S.806 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: S.707, A.709, E.1075, N.1077 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain C: N.1101, T.1103, H.1104, F.1106 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain C: N.1137 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain D: N.126, T.128 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain D: E.284, N.285 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain D: N.619, T.621, Q.647 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain D: N.712, G.1134 Chain E: D.799 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain D: N.720, L.925, Q.929, Q.1074 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.925 NAG-NAG.17: 4 residues within 4Å: Chain D: N.804, S.806, Q.807, F.820 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.820 NAG-NAG.18: 3 residues within 4Å: Chain D: A.709, E.1075, N.1077 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:A.709 NAG-NAG.19: 4 residues within 4Å: Chain D: N.1101, T.1103, H.1104, F.1106 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain D: N.1137 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain E: T.112, N.237, T.239 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain E: E.284, N.285 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain E: N.334, P.582, Q.583, L.585 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 2 residues within 4Å: Chain E: G.342, N.346 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain C: D.851, I.853 Chain E: N.619, Q.647 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain C: D.799 Chain E: N.712, G.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain E: N.720, L.925, Q.1074 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:L.925 NAG-NAG.28: 2 residues within 4Å: Chain E: N.804, S.806 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 2 residues within 4Å: Chain E: E.1075, N.1077 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 4 residues within 4Å: Chain E: N.1101, T.1103, H.1104, F.1106 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 1 residues within 4Å: Chain E: N.1137 No protein-ligand interaction detected (PLIP)

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

NAG.32: 2 residues within 4Å: Chain C: Y.34, N.67 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.168 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: G.235, I.236, N.237 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.606, T.607 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: H.658, N.660 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain D: Y.34, N.67 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: R.360 Chain D: N.168 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain D: G.235, N.237 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain D: N.334, Q.583, T.584 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain D: N.606, T.607 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain D: N.660 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain E: N.36, N.67 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain E: N.126, A.127, N.129, F.160 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain E: S.116, N.167, N.168 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain E: N.606 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain E: N.660 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kocharovskaya, M.V. et al., Structure and dynamics of Alpha B.1.1.7 SARS-CoV-2 S-protein in complex with Fab of neutralizing antibody REGN10987. Biochem.Biophys.Res.Commun. (2025)

Release Date

2025-04-02

Peptides

REGN10987 Fab homologue (Light chain): AFH
REGN10987 Fab homologue (Heavy chain): BGI
Spike glycoprotein: CDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
i

F
g

H
l

B
j

G
h

I
n

C
A

D
B

E
C

REGN10987 Fab homologue (Light chain)

REGN10987 Fab homologue (Heavy chain)

Spike glycoprotein

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