SMTL ID : 7jjj.1

Structure of SARS-CoV-2 3Q-2P full-length dimers of spike trimers

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

76 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: 3 residues within 4Å: Chain A: Y.28, T.29, N.61 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: F.338, G.339, N.343, S.371 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.370, A:S.371 NAG-NAG.3: 5 residues within 4Å: Chain A: N.717, N.919, L.922, N.925, Q.1071 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.922, A:N.925 Hydrogen bonds: A:N.925 NAG-NAG.4: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.804 NAG-NAG.5: 5 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 Chain C: Q.895 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.1098, G.1099, T.1100, H.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 6 residues within 4Å: Chain A: N.122, N.125, V.127, E.154, F.157, V.171 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 9 residues within 4Å: Chain A: T.108, N.234, T.236 Chain B: R.457, K.458, S.459, N.460, K.462, E.465 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain A: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain A: N.164, N.165 Chain B: Y.351, I.468 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain A: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain A: Y.144, H.146, N.148, N.149, S.151 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain B: Y.28, T.29, N.61 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain B: N.616, T.618, Q.644, T.645, R.646 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 5 residues within 4Å: Chain B: F.338, G.339, N.343, N.370, S.371 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.370 NAG-NAG.17: 3 residues within 4Å: Chain B: N.709, N.710, G.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain B: N.717, L.922, N.925, Q.926 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.922, B:N.925, B:Q.926 Hydrogen bonds: B:N.925 NAG-NAG.19: 1 residues within 4Å: Chain B: N.801 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain B: A.706, E.1072, K.1073, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain B: N.1098, G.1099, T.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain B: C.1082, I.1132, V.1133, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 6 residues within 4Å: Chain B: N.122, A.123, N.125, V.127, E.154, V.171 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.171 NAG-NAG.24: 8 residues within 4Å: Chain B: T.108, N.234, T.236 Chain C: R.457, K.458, S.459, N.460, E.465 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 5 residues within 4Å: Chain B: N.164, N.165 Chain C: Y.351, A.352, I.468 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 5 residues within 4Å: Chain B: C.15, V.16, N.17, C.136, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 5 residues within 4Å: Chain B: Y.144, K.147, N.149, S.151, M.153 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.144 Hydrogen bonds: B:Y.144 NAG-NAG.28: 6 residues within 4Å: Chain B: I.834 Chain C: N.616, T.618, Q.644, T.645, R.646 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 2 residues within 4Å: Chain C: N.709, N.710 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 4 residues within 4Å: Chain C: N.717, L.922, N.925, Q.926 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.922, C:N.925, C:Q.926 NAG-NAG.31: 4 residues within 4Å: Chain C: N.801, S.803, Q.804, F.817 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.817 NAG-NAG.32: 4 residues within 4Å: Chain C: A.706, E.1072, K.1073, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 4 residues within 4Å: Chain C: N.1098, G.1099, T.1100, H.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 4 residues within 4Å: Chain C: C.1082, I.1132, V.1133, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 5 residues within 4Å: Chain C: N.122, A.123, N.125, V.127, V.171 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.171 NAG-NAG.36: 7 residues within 4Å: Chain A: R.457, K.458, S.459, N.460, E.465 Chain C: N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 3 residues within 4Å: Chain A: I.468 Chain C: N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 4 residues within 4Å: Chain C: C.15, V.16, N.17, C.136 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 5 residues within 4Å: Chain C: Y.145, N.148, N.149, S.151, M.153 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.145 NAG-NAG.41: 3 residues within 4Å: Chain D: Y.28, T.29, N.61 No protein-ligand interaction detected (PLIP) NAG-NAG.42: 4 residues within 4Å: Chain D: F.338, G.339, N.343, S.371 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.370, D:S.371 NAG-NAG.43: 5 residues within 4Å: Chain D: N.717, N.919, L.922, N.925, Q.1071 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.922, D:N.925 Hydrogen bonds: D:N.925 NAG-NAG.44: 3 residues within 4Å: Chain D: N.801, S.803, Q.804 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.804 NAG-NAG.45: 5 residues within 4Å: Chain D: A.706, E.1072, K.1073, N.1074 Chain F: Q.895 No protein-ligand interaction detected (PLIP) NAG-NAG.46: 4 residues within 4Å: Chain D: N.1098, G.1099, T.1100, H.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.47: 6 residues within 4Å: Chain D: N.122, N.125, V.127, E.154, F.157, V.171 No protein-ligand interaction detected (PLIP) NAG-NAG.48: 9 residues within 4Å: Chain D: T.108, N.234, T.236 Chain E: R.457, K.458, S.459, N.460, K.462, E.465 No protein-ligand interaction detected (PLIP) NAG-NAG.49: 3 residues within 4Å: Chain D: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.50: 4 residues within 4Å: Chain D: N.164, N.165 Chain E: Y.351, I.468 No protein-ligand interaction detected (PLIP) NAG-NAG.51: 3 residues within 4Å: Chain D: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.52: 5 residues within 4Å: Chain D: Y.144, H.146, N.148, N.149, S.151 No protein-ligand interaction detected (PLIP) NAG-NAG.54: 3 residues within 4Å: Chain E: Y.28, T.29, N.61 No protein-ligand interaction detected (PLIP) NAG-NAG.55: 5 residues within 4Å: Chain E: N.616, T.618, Q.644, T.645, R.646 No protein-ligand interaction detected (PLIP) NAG-NAG.56: 5 residues within 4Å: Chain E: F.338, G.339, N.343, N.370, S.371 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.370 NAG-NAG.57: 3 residues within 4Å: Chain E: N.709, N.710, G.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.58: 4 residues within 4Å: Chain E: N.717, L.922, N.925, Q.926 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:L.922, E:N.925, E:Q.926 Hydrogen bonds: E:N.925 NAG-NAG.59: 1 residues within 4Å: Chain E: N.801 No protein-ligand interaction detected (PLIP) NAG-NAG.60: 4 residues within 4Å: Chain E: A.706, E.1072, K.1073, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.61: 3 residues within 4Å: Chain E: N.1098, G.1099, T.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.62: 4 residues within 4Å: Chain E: C.1082, I.1132, V.1133, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.63: 6 residues within 4Å: Chain E: N.122, A.123, N.125, V.127, E.154, V.171 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.171 NAG-NAG.64: 8 residues within 4Å: Chain E: T.108, N.234, T.236 Chain F: R.457, K.458, S.459, N.460, E.465 No protein-ligand interaction detected (PLIP) NAG-NAG.65: 5 residues within 4Å: Chain E: N.164, N.165 Chain F: Y.351, A.352, I.468 No protein-ligand interaction detected (PLIP) NAG-NAG.66: 5 residues within 4Å: Chain E: C.15, V.16, N.17, C.136, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.67: 5 residues within 4Å: Chain E: Y.144, K.147, N.149, S.151, M.153 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:Y.144 Hydrogen bonds: E:Y.144 NAG-NAG.68: 6 residues within 4Å: Chain E: I.834 Chain F: N.616, T.618, Q.644, T.645, R.646 No protein-ligand interaction detected (PLIP) NAG-NAG.69: 2 residues within 4Å: Chain F: N.709, N.710 No protein-ligand interaction detected (PLIP) NAG-NAG.70: 4 residues within 4Å: Chain F: N.717, L.922, N.925, Q.926 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:L.922, F:N.925, F:Q.926 NAG-NAG.71: 4 residues within 4Å: Chain F: N.801, S.803, Q.804, F.817 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:F.817 NAG-NAG.72: 4 residues within 4Å: Chain F: A.706, E.1072, K.1073, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.73: 4 residues within 4Å: Chain F: N.1098, G.1099, T.1100, H.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.74: 4 residues within 4Å: Chain F: C.1082, I.1132, V.1133, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.75: 5 residues within 4Å: Chain F: N.122, A.123, N.125, V.127, V.171 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:V.171 NAG-NAG.76: 7 residues within 4Å: Chain D: R.457, K.458, S.459, N.460, E.465 Chain F: N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.77: 3 residues within 4Å: Chain D: I.468 Chain F: N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.78: 4 residues within 4Å: Chain F: C.15, V.16, N.17, C.136 No protein-ligand interaction detected (PLIP) NAG-NAG.79: 5 residues within 4Å: Chain F: Y.145, N.148, N.149, S.151, M.153 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:Y.145

2 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.13: 6 residues within 4Å: Chain A: N.616, T.618, V.620 Chain C: F.833, I.834, Q.836 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.618 NAG-NAG-FUC.53: 6 residues within 4Å: Chain D: N.616, T.618, V.620 Chain F: F.833, I.834, Q.836 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.618

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

NAG-NAG-BMA-FUC.40: 6 residues within 4Å: Chain C: N.280, E.281, N.282 Chain F: P.209, F.220, T.286 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:F.220 NAG-NAG-BMA-FUC.80: 6 residues within 4Å: Chain C: P.209, F.220, T.286 Chain F: N.280, E.281, N.282 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:F.220

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

NAG.81: 3 residues within 4Å: Chain A: N.331, I.332, T.333 Ligand excluded by PLIP NAG.82: 3 residues within 4Å: Chain A: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.83: 3 residues within 4Å: Chain A: I.1132, V.1133, N.1134 Ligand excluded by PLIP NAG.84: 1 residues within 4Å: Chain B: N.331 Ligand excluded by PLIP NAG.85: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.86: 3 residues within 4Å: Chain C: Y.28, T.29, N.61 Ligand excluded by PLIP NAG.87: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.88: 6 residues within 4Å: Chain C: F.338, G.339, N.343, V.367, L.368, S.371 Ligand excluded by PLIP NAG.89: 3 residues within 4Å: Chain D: N.331, I.332, T.333 Ligand excluded by PLIP NAG.90: 3 residues within 4Å: Chain D: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.91: 3 residues within 4Å: Chain D: I.1132, V.1133, N.1134 Ligand excluded by PLIP NAG.92: 1 residues within 4Å: Chain E: N.331 Ligand excluded by PLIP NAG.93: 3 residues within 4Å: Chain E: N.280, E.281, N.282 Ligand excluded by PLIP NAG.94: 3 residues within 4Å: Chain F: Y.28, T.29, N.61 Ligand excluded by PLIP NAG.95: 2 residues within 4Å: Chain F: N.331, Q.580 Ligand excluded by PLIP NAG.96: 6 residues within 4Å: Chain F: F.338, G.339, N.343, V.367, L.368, S.371 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bangaru, S. et al., Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate. Science (2020)

Release Date

2020-08-26

Peptides

Spike glycoprotein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Spike glycoprotein

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