SMTL ID : 7sbt.1

One RBD-up 2 of pre-fusion SARS-CoV-2 Gamma variant spike protein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.40 Å

Oligo State

homo-trimer

Ligands

17 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: 2 residues within 4Å: Chain A: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.616, T.618, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.717, L.922, Q.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.4: 2 residues within 4Å: Chain A: N.801, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain B: N.122, T.124, N.125, E.154, V.171 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.171 NAG-NAG.10: 2 residues within 4Å: Chain B: E.132, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain B: N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain B: N.616, T.618, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain B: N.717, L.922, Q.1071 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG.14: 2 residues within 4Å: Chain B: N.801, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 5 residues within 4Å: Chain C: N.122, T.124, N.125, E.154, V.171 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.171 NAG-NAG.20: 3 residues within 4Å: Chain C: E.132, N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain B: K.458, E.465 Chain C: T.108, N.234, T.236 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.236 NAG-NAG.22: 4 residues within 4Å: Chain B: K.558 Chain C: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 2 residues within 4Å: Chain A: I.834 Chain C: N.616 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain C: N.717, L.922, Q.1071 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 NAG-NAG.25: 2 residues within 4Å: Chain C: N.801, S.803 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.5: 1 residues within 4Å: Chain A: N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.15: 1 residues within 4Å: Chain B: N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.26: 1 residues within 4Å: Chain C: N.1074 No protein-ligand interaction detected (PLIP)

9 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.6: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.7: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.8: 7 residues within 4Å: Chain A: T.19, N.20, T.73, N.74, G.75, T.76, K.77 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.20 NAG-NAG-MAN.16: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.17: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.18: 3 residues within 4Å: Chain B: N.20, N.74, K.77 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:K.77 Hydrogen bonds: B:N.20, B:N.20 NAG-NAG-MAN.27: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.28: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.29: 3 residues within 4Å: Chain C: N.20, N.74, K.77 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.20

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

NAG.30: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain A: N.122, T.124, N.125, V.127, E.154 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain A: K.147, N.148, N.149, M.153 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: E.132, N.164, N.165 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: N.234, T.236 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain A: N.282 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain A: N.343, V.367, F.374 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain A: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain A: Y.1155, N.1158 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain B: K.147, N.148, N.149, M.153 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain B: N.234 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain B: N.331 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain B: F.338, G.339, N.343 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain B: N.709, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain B: N.1158 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain C: N.61 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain C: K.147, N.149, M.153 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain C: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain C: G.339, N.343, V.367 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain C: N.709, N.710 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain C: N.1158 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, J. et al., Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant. Science (2021)

Release Date

2021-11-10

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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