SMTL ID : 7vhh.1

Delta variant of SARS-CoV-2 Spike protein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

12 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: I.703, N.704, L.909, Q.913, Q.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: I.1119, N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: I.703, N.704, L.909, Q.913 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain B: I.1119, N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain C: I.703, N.704, L.909, Q.913, Q.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: N.1085, T.1087, H.1088 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain C: I.1119, N.1121 No protein-ligand interaction detected (PLIP)

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

NAG.13: 6 residues within 4Å: Chain A: N.109, T.111, N.112, V.114, E.141, F.144 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: E.268, N.269 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.318, I.319, Q.567 Ligand excluded by PLIP NAG.16: 5 residues within 4Å: Chain A: G.326, F.329, N.330, S.360, F.361 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: E.296, K.297, N.590, T.591 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.603, T.605, Q.631 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.644 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: N.696, N.697, G.1118 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: A.693, E.1059, K.1060, N.1061 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: S.99, E.119, N.151, N.152 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: T.95, N.221, T.223 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: Y.15, N.48 Ligand excluded by PLIP NAG.25: 6 residues within 4Å: Chain B: N.109, T.111, N.112, V.114, K.116, F.144 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: N.269, T.271 Chain C: K.545 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.318, Q.567 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: G.326, F.329, N.330, S.360 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.590, T.591 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.603, Q.631 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: H.642, N.644 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain A: D.783, G.785 Chain B: N.696, I.1117 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain B: A.693, E.1059, K.1060, N.1061 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain B: S.99, E.119, N.151, N.152 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: T.95, N.221 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: Y.15, N.48 Ligand excluded by PLIP NAG.37: 6 residues within 4Å: Chain C: N.109, T.111, N.112, V.114, E.141, F.144 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: N.267, N.269 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.318, Q.567 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain C: G.326, E.327, N.330, S.360 Ligand excluded by PLIP NAG.41: 5 residues within 4Å: Chain C: V.295, E.296, G.588, T.589, N.590 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.603, T.605, Q.631 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: H.642, V.643, N.644 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain B: D.783 Chain C: N.696, N.697 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain C: A.693, E.1059, K.1060, N.1061 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: N.151, N.152 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.221 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, X., Structure of delta variant SARS-CoV-2 Spike protein. To Be Published

Release Date

2022-12-28

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

Spike glycoprotein

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