SMTL ID : 7sbp.1

Closed state of pre-fusion SARS-CoV-2 Kappa variant spike protein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.10 Å

Oligo State

homo-trimer

Ligands

6 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.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.616, T.618 Chain B: I.834, Q.836 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain B: C.15, N.17 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain B: N.616, T.618 Chain C: I.834, Q.836 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain C: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 4 residues within 4Å: Chain A: I.834, Q.836 Chain C: N.616, Q.644 No protein-ligand interaction detected (PLIP)

27 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.2: 5 residues within 4Å: Chain A: N.122, A.123, T.124, N.125, V.127 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.3: 6 residues within 4Å: Chain A: T.108, N.234, T.236 Chain C: R.457, K.462, E.465 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.236 NAG-NAG-MAN.4: 3 residues within 4Å: Chain A: E.281, N.282 Chain C: K.558 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.6: 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-MAN.7: 2 residues within 4Å: Chain A: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.9: 3 residues within 4Å: Chain A: N.1098, T.1100, D.1101 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.10: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.11: 4 residues within 4Å: Chain A: N.164, N.165 Chain C: Y.351, I.468 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.12: 3 residues within 4Å: Chain A: G.339, N.343 Chain C: Y.489 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.489 NAG-NAG-MAN.14: 5 residues within 4Å: Chain B: N.122, A.123, T.124, N.125, V.127 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.15: 7 residues within 4Å: Chain A: R.457, K.458, K.462, E.465 Chain B: T.108, N.234, T.236 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.458 NAG-NAG-MAN.16: 2 residues within 4Å: Chain B: E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.18: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.19: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.21: 4 residues within 4Å: Chain B: N.1098, T.1100, D.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.22: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.23: 3 residues within 4Å: Chain A: Y.351 Chain B: N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.24: 3 residues within 4Å: Chain A: Y.489 Chain B: G.339, N.343 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.489 NAG-NAG-MAN.26: 4 residues within 4Å: Chain C: N.122, T.124, N.125, V.127 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.27: 6 residues within 4Å: Chain B: R.457, K.462, E.465 Chain C: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.28: 3 residues within 4Å: Chain B: K.558 Chain C: E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.30: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.31: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.33: 4 residues within 4Å: Chain C: N.1098, T.1100, D.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.34: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.35: 2 residues within 4Å: Chain C: N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.36: 4 residues within 4Å: Chain B: Y.489 Chain C: F.338, G.339, N.343 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.489

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.8: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.20: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.32: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP)

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

NAG.37: 2 residues within 4Å: Chain A: F.59, N.61 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain A: N.148, N.149 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain A: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain A: N.709, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain A: N.1158 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain B: N.61 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain B: K.147, N.148, N.149 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain B: P.330, N.331, P.579, Q.580 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain B: N.709, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain B: N.1158 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain C: F.59, N.61 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain C: K.147, N.148, N.149 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain C: P.330, N.331, P.579, Q.580 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain C: N.1158, H.1159 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

2021-11-03

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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