SMTL ID : 7zss.1

cryo-EM structure of D614 spike in complex with de novo designed binder

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

7 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: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.2: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG.3: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain C: A.706, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain C: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922

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

NAG.8: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.801, S.803 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: E.1072, N.1074 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.616, T.618, R.646 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: T.124, N.125, V.127 Ligand excluded by PLIP NAG.16: 5 residues within 4Å: Chain A: S.112, K.113, E.132, N.164, N.165 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: N.709, I.1130 Chain C: D.796 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.801, S.803 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: N.122, T.124, N.125 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: E.132, N.164, N.165 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.616, Q.644 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: E.281, N.282 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain B: I.468 Chain C: S.112, E.132, N.164, N.165 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain C: N.122, T.124, N.125, V.127, Y.160 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain C: N.331, P.579, Q.580, L.582 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: N.603, T.604 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: N.616, T.618, Q.644 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gainza, P. et al., De novo design of protein interactions with learned surface fingerprints. Nature (2023)

Release Date

2023-03-01

Peptides

Spike glycoprotein: ABC
de novo designed binder: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
P

F
h

Spike glycoprotein

de novo designed binder

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