SMTL ID : 7zrv.1

cryo-EM structure of omicron spike in complex with de novo designed binder, full map

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-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: 3 residues within 4Å: Chain A: N.328, Q.577, T.578 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.578 NAG-NAG.3: 2 residues within 4Å: Chain A: N.706 Chain C: Y.793 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain A: N.277, E.278, N.279 Chain B: K.555 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain A: N.120, A.121, T.122, N.123, V.125, F.152 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 6 residues within 4Å: Chain A: T.106, N.231, T.233 Chain B: K.455, S.456, K.459 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain A: I.791, Y.793 Chain B: N.706 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain B: D.336, F.339, N.340, L.368 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain B: E.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain B: N.120, A.121, N.123, M.148 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain B: Q.113, E.130, N.159, N.160 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 2 residues within 4Å: Chain C: E.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 2 residues within 4Å: Chain B: Y.793 Chain C: N.706 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 2 residues within 4Å: Chain C: N.328, Q.577 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 4 residues within 4Å: Chain C: D.336, F.339, N.340, L.368 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 5 residues within 4Å: Chain C: N.120, T.122, N.123, V.125, F.152 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 4 residues within 4Å: Chain C: K.111, E.130, N.159, N.160 No protein-ligand interaction detected (PLIP)

12 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 4 residues within 4Å: Chain A: F.339, N.340, V.364, L.368 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 3 residues within 4Å: Chain A: N.714, L.919, Q.1068 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.919 NAG-NAG-BMA.6: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 5 residues within 4Å: Chain A: N.159, N.160 Chain E: L.29, E.30, N.31 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.30 NAG-NAG-BMA.12: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 3 residues within 4Å: Chain B: N.714, L.919, Q.1068 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.919 NAG-NAG-BMA.14: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 3 residues within 4Å: Chain C: N.714, L.919, Q.1068 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.919 NAG-NAG-BMA.24: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP)

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

NAG.31: 1 residues within 4Å: Chain A: N.654 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain A: N.613, T.615, E.616 Chain C: Q.833 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain A: N.600 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain A: Q.892 Chain B: A.703, N.1071 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: Y.652, N.654 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain A: Y.834, D.836 Chain B: N.613, T.615, E.616 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain B: N.328, Q.577, T.578, L.579 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain B: N.231 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain B: N.600 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.600, T.601 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: A.703, N.1071 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.654 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain A: E.462 Chain C: T.106, N.231, T.233 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

2023-03-08

Peptides

Spike glycoprotein,Envelope glycoprotein: ABC
de novo designed binder: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
F

Spike glycoprotein,Envelope glycoprotein

de novo designed binder

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