SMTL ID : 7jzn.1

SARS-CoV-2 spike in complex with LCB3 (2RBDs open)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

13 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: 5 residues within 4Å: Chain A: N.717, L.922, N.925, Q.926, Q.1071 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.922, A:N.925 NAG-NAG.2: 2 residues within 4Å: Chain A: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain C: T.108, N.234 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 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 NAG-NAG.7: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain E: N.717, L.922, Q.926 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:L.922, E:Q.926 NAG-NAG.11: 3 residues within 4Å: Chain E: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain E: N.1098, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain E: I.1132, N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.14: 4 residues within 4Å: Chain A: Y.28, T.29, N.30, N.61 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.122, A.123, V.127 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: G.232, N.234 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.280, N.282 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: F.338, G.339, N.343, V.367 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: N.603, T.604 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.616, Q.644 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain C: F.59, N.61 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain C: N.122, A.123, T.124, V.127 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: N.280, N.282 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain C: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: A.706, N.1074 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain E: N.61 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain E: N.122, T.124, N.125 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain E: N.234 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain E: N.282 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain E: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain E: G.339, F.342, N.343 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain E: N.603 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain E: N.616, Q.644 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain E: N.657 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain E: N.709, G.1131 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain A: Q.895 Chain E: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain E: E.132, N.165 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, L. et al., De novo design of picomolar SARS-CoV-2 miniprotein inhibitors. Science (2020)

Release Date

2020-09-23

Peptides

Spike glycoprotein: ACE
LCB3: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

E
C

B
E

D
F

F
G

Spike glycoprotein

LCB3

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