SMTL ID : 7vrw.1

VAS5 Spike (3 RBD down)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.60 Å

Oligo State

homo-trimer

Ligands

14 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: T.96, N.222, T.224 Chain B: R.445, S.447 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.698, L.903, Q.907, Q.1052 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.782, S.784, Q.785, F.798 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.798 NAG-NAG.4: 4 residues within 4Å: Chain A: N.1079, T.1081, H.1082, F.1084 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.1115 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.698, L.903, N.906, Q.907 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.782, S.784, Q.785 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain B: N.1079, G.1080, T.1081, H.1082, F.1084 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain B: I.1113, N.1115 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain A: K.450 Chain C: T.96, N.222, T.224 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain C: N.698, L.903 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain C: N.782, S.784, Q.785, F.798 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.798 NAG-NAG.13: 3 residues within 4Å: Chain C: N.1079, H.1082, F.1084 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain C: D.1108, N.1115 No protein-ligand interaction detected (PLIP)

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

NAG.15: 3 residues within 4Å: Chain A: N.268, E.269, N.270 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.319, Q.568 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: G.327, E.328, N.331 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: G.589, N.591, T.592 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: H.643, V.644, N.645 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: N.690, N.691 Chain C: D.777 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: A.687, E.1053, K.1054, N.1055 Ligand excluded by PLIP NAG.22: 6 residues within 4Å: Chain A: F.580, D.602, V.603, N.604 Chain C: K.835, F.836 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: Y.16, N.18, F.47, N.49 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: F.47, N.49 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: E.269, N.270 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.319, Q.568 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.331 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: E.297, N.591 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.604 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: H.643, N.645 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: D.777 Chain B: N.690, N.691 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain B: A.687, E.1053, K.1054, N.1055 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain B: N.153 Chain C: Y.339, A.340, I.456 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain B: T.96, N.222, T.224 Chain C: R.445, K.450 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain C: Y.16, N.18, F.47, N.49 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: E.269, N.270 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.319, S.518, Q.568 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: N.331, A.332, L.429 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.591, T.592 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.604, T.606 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: H.643, V.644, N.645 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.690, N.691, G.1112 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain B: Q.876 Chain C: A.687, E.1053, K.1054, N.1055 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhen, C. et al., VAS5 Spike (3-RBD down). To Be Published

Release Date

2022-06-22

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

Spike glycoprotein

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