SMTL ID : 8hxj.1

BANAL-20-52 Spike trimer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

24 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: 8 residues within 4Å: Chain A: T.108, N.234 Chain C: R.457, K.458, S.459, N.460, K.462, E.465 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.458 NAG-NAG.2: 5 residues within 4Å: Chain A: S.112, E.132, N.164, N.165 Chain C: Y.351 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.164 NAG-NAG.3: 6 residues within 4Å: Chain A: N.122, N.125, K.129, S.155, E.156, F.157 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.713, N.921, Q.1067 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain A: N.797, S.799 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: A.702, E.1068, N.1070 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain A: N.1130 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 8 residues within 4Å: Chain A: R.457, K.458, S.459, N.460, K.462, E.465 Chain B: T.108, N.234 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.458 NAG-NAG.10: 4 residues within 4Å: Chain A: Y.351 Chain B: E.132, N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain B: N.797, S.799 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain B: N.1130 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain B: S.700, A.702, N.1070 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.700 NAG-NAG.14: 5 residues within 4Å: Chain B: N.122, A.123, N.125, V.127, S.155 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain B: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain B: N.713, Q.1067 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 8 residues within 4Å: Chain B: R.457, K.458, S.459, N.460, K.462, E.465 Chain C: T.108, N.234 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.458 NAG-NAG.18: 2 residues within 4Å: Chain C: N.797, S.799 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain C: A.702, N.1070 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 2 residues within 4Å: Chain C: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain C: N.713, L.918, N.921, Q.922, Q.1067 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.918, C:N.921 Hydrogen bonds: C:N.921 NAG-NAG.22: 2 residues within 4Å: Chain C: N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 7 residues within 4Å: Chain C: N.122, A.123, N.125, V.127, K.129, S.155, E.169 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 1 residues within 4Å: Chain C: N.1130 No protein-ligand interaction detected (PLIP)

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

NAG.25: 3 residues within 4Å: Chain A: C.15, N.17, N.137 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: N.616, E.619 Chain B: Q.832, G.834 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: H.655, V.656, N.657 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain A: N.343, S.371 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain A: N.370 Chain C: L.455, F.456, Y.489, F.490 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain A: N.30, F.59 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain A: N.705, I.1126, G.1127 Chain B: D.792 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: N.1094, G.1095, H.1097 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: H.655, V.656, N.657 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: N.616 Chain C: Q.832 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: N.30, F.59 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain B: N.705, I.1126, G.1127 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain B: N.1094, G.1095, F.1099, Y.1106, P.1108 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain B: N.343, S.371 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain B: C.15, N.17, N.137 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain A: Q.493 Chain B: N.370 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain C: C.15, N.17, C.136, N.137 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain C: H.655, V.656, N.657 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: N.343, S.371 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain C: N.705, I.1126, G.1127 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.54: 5 residues within 4Å: Chain C: N.1094, H.1097, F.1099, Y.1106, P.1108 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain C: N.30, F.59 Ligand excluded by PLIP NAG.57: 5 residues within 4Å: Chain B: L.455, F.456, F.490, Q.493 Chain C: N.370 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, X. et al., The selective effect of fecal-oral transmission on the S proteins of bat SARS-CoV-2 related coronaviruses in favor of stability over infectivity. To Be Published

Release Date

2024-01-10

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein