SMTL ID : 7jji.1

Structure of SARS-CoV-2 3Q-2P full-length prefusion spike trimer (C3 symmetry)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

45 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 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.28 NAG-NAG.2: 5 residues within 4Å: Chain A: N.616, T.618, Q.644, T.645 Chain C: I.834 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: F.338, G.339, N.343, S.371 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.709, G.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: N.717, L.922 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.6: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain A: E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain A: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain A: I.1132, V.1133, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain A: N.122, A.123, N.125, V.127, V.171 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.171 NAG-NAG.11: 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.12: 3 residues within 4Å: Chain A: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain A: N.164, N.165 Chain B: Y.351, I.468 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain A: C.15, V.16, N.17 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain A: H.146, N.148, N.149, S.151, M.153 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain B: Y.28, T.29, N.61 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.28 NAG-NAG.17: 5 residues within 4Å: Chain A: I.834 Chain B: N.616, T.618, Q.644, T.645 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain B: F.338, G.339, N.343, S.371 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain B: N.709, G.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 2 residues within 4Å: Chain B: N.717, L.922 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG.21: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain B: E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 5 residues within 4Å: Chain B: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain B: I.1132, V.1133, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 5 residues within 4Å: Chain B: N.122, A.123, N.125, V.127, V.171 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.171 NAG-NAG.26: 9 residues within 4Å: Chain B: T.108, N.234, T.236 Chain C: R.457, K.458, S.459, N.460, K.462, E.465 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain B: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 4 residues within 4Å: Chain B: N.164, N.165 Chain C: Y.351, I.468 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 3 residues within 4Å: Chain B: C.15, V.16, N.17 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 5 residues within 4Å: Chain B: H.146, N.148, N.149, S.151, M.153 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 3 residues within 4Å: Chain C: Y.28, T.29, N.61 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.28 NAG-NAG.32: 5 residues within 4Å: Chain B: I.834 Chain C: N.616, T.618, Q.644, T.645 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 4 residues within 4Å: Chain C: F.338, G.339, N.343, S.371 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 2 residues within 4Å: Chain C: N.709, G.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 2 residues within 4Å: Chain C: N.717, L.922 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 NAG-NAG.36: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 2 residues within 4Å: Chain C: E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 5 residues within 4Å: Chain C: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 3 residues within 4Å: Chain C: I.1132, V.1133, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.40: 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.41: 9 residues within 4Å: Chain A: R.457, K.458, S.459, N.460, K.462, E.465 Chain C: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.42: 3 residues within 4Å: Chain C: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.43: 4 residues within 4Å: Chain A: Y.351, I.468 Chain C: N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.44: 3 residues within 4Å: Chain C: C.15, V.16, N.17 No protein-ligand interaction detected (PLIP) NAG-NAG.45: 5 residues within 4Å: Chain C: H.146, N.148, N.149, S.151, M.153 No protein-ligand interaction detected (PLIP)

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

NAG.46: 2 residues within 4Å: Chain A: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG.50: 2 residues within 4Å: Chain B: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG.53: 2 residues within 4Å: Chain C: N.331, Q.580 No protein-ligand interaction detected (PLIP)

3 x VCG: 2-hydroxyethyl 2-deoxy-3,5-bis-O-(2-hydroxyethyl)-6-O-(2-{[(9E)-octadec-9-enoyl]oxy}ethyl)-alpha-L-xylo-hexofuranoside(Non-covalent)

VCG.47: 15 residues within 4Å: Chain A: I.101, R.102, G.103, W.104, I.119, N.121, V.126, I.128, F.168, Y.170, S.172, R.190, H.207, V.227, L.229 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.104, A:I.119, A:N.121, A:V.126, A:F.168, A:Y.170, A:V.227, A:L.229 Hydrogen bonds: A:N.121, A:S.172, A:R.190 Salt bridges: A:R.190 VCG.51: 15 residues within 4Å: Chain B: I.101, R.102, G.103, W.104, I.119, N.121, V.126, I.128, F.168, Y.170, S.172, R.190, H.207, V.227, L.229 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.104, B:I.119, B:N.121, B:V.126, B:F.168, B:Y.170, B:V.227, B:L.229 Hydrogen bonds: B:N.121, B:S.172, B:R.190 Salt bridges: B:R.190 VCG.54: 15 residues within 4Å: Chain C: I.101, R.102, G.103, W.104, I.119, N.121, V.126, I.128, F.168, Y.170, S.172, R.190, H.207, V.227, L.229 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:W.104, C:I.119, C:N.121, C:V.126, C:F.168, C:Y.170, C:V.227, C:L.229 Hydrogen bonds: C:N.121, C:S.172, C:R.190 Salt bridges: C:R.190

3 x EIC: LINOLEIC ACID(Non-covalent)

EIC.48: 15 residues within 4Å: Chain A: Q.409, G.416, K.417 Chain C: C.336, F.338, I.358, Y.365, Y.369, A.372, F.374, F.377, V.395, I.434, L.513, V.524 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:F.338, C:I.358, C:Y.365, C:Y.365, C:Y.365, C:Y.365, C:Y.369, C:F.377, C:V.395, C:I.434, C:L.513, C:V.524 Hydrogen bonds: C:A.372, A:Q.409, A:K.417 Salt bridges: A:K.417 EIC.49: 15 residues within 4Å: Chain A: C.336, F.338, I.358, Y.365, Y.369, A.372, F.374, F.377, V.395, I.434, L.513, V.524 Chain B: Q.409, G.416, K.417 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.338, A:I.358, A:Y.365, A:Y.365, A:Y.365, A:Y.365, A:Y.369, A:F.377, A:V.395, A:I.434, A:L.513, A:V.524 Hydrogen bonds: A:A.372, B:Q.409, B:K.417 Salt bridges: B:K.417 EIC.52: 15 residues within 4Å: Chain B: C.336, F.338, I.358, Y.365, Y.369, A.372, F.374, F.377, V.395, I.434, L.513, V.524 Chain C: Q.409, G.416, K.417 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:F.338, B:I.358, B:Y.365, B:Y.365, B:Y.365, B:Y.365, B:Y.369, B:F.377, B:V.395, B:I.434, B:L.513, B:V.524 Hydrogen bonds: B:A.372, C:Q.409, C:K.417 Salt bridges: C:K.417

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: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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