SMTL ID : 7jzl.1

SARS-CoV-2 spike in complex with LCB1 (2RBDs open)

Coordinates

PDB Format Compare

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: 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 A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 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.6: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain A: K.462 Chain E: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain E: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:L.922 NAG-NAG.11: 4 residues within 4Å: Chain E: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain E: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain E: N.801, Q.804 No protein-ligand interaction detected (PLIP)

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

NAG.14: 2 residues within 4Å: Chain A: G.232, N.234 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: T.29, N.30, N.61 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.122, A.123, T.124 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.282 Chain C: K.558 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.19: 5 residues within 4Å: Chain A: F.338, G.339, F.342, N.343, L.368 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.616, Q.644 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: H.655, V.656, N.657 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: N.709, I.1130, 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: G.232, N.234 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: Y.28, F.59, N.61 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain C: N.122, A.123, V.127 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: N.280, N.282 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: N.331, Q.580, L.582 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain C: N.343 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: N.616, Q.644 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: H.655, V.656, N.657 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain A: Q.895 Chain C: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain E: Y.28, F.59, N.61 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain E: N.122, A.123, V.127 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain E: N.280, E.281, 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, N.343, S.373 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain E: N.603 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain E: N.616 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain E: H.655, V.656, N.657 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain E: N.709, G.1131 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain E: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain A: Y.351 Chain E: N.164, 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
LCB1: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
B

B
E

D
G

F
F

Spike glycoprotein

LCB1

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