SMTL ID : 7z3z.1

Locked Wuhan SARS-CoV2 Prefusion Spike ectodomain with lipid bound

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

15 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: 10 residues within 4Å: Chain A: T.108, N.234, T.236 Chain C: R.457, K.458, S.459, N.460, L.461, K.462, E.465 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: N.717, L.922, N.925, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.3: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: G.1085, D.1127, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 10 residues within 4Å: Chain A: R.457, K.458, S.459, N.460, L.461, K.462, E.465 Chain B: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain B: N.717, L.922, N.925, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG.8: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain B: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: G.1085, D.1127, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 10 residues within 4Å: Chain B: R.457, K.458, S.459, N.460, L.461, K.462, E.465 Chain C: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain C: N.717, L.922, N.925, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 NAG-NAG.13: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain C: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: G.1085, D.1127, N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.16: 3 residues within 4Å: Chain A: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.17: 6 residues within 4Å: Chain A: N.122, T.124, N.125, V.127, E.154, F.157 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: N.331, P.579, Q.580, L.582 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: N.343, A.344, T.345, S.371 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.603, T.604 Ligand excluded by PLIP NAG.22: 7 residues within 4Å: Chain A: N.616, T.618, E.619, Q.644, T.645, R.646 Chain B: I.834 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.24: 6 residues within 4Å: Chain A: N.709, N.710, I.1130, G.1131 Chain B: I.794, D.796 Ligand excluded by PLIP NAG.25: 6 residues within 4Å: Chain A: A.706, A.713, E.1072, K.1073, N.1074 Chain B: Q.895 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: N.164, N.165 Chain C: Y.351, I.468 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain A: C.15, N.17, T.19, N.137 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.30: 6 residues within 4Å: Chain B: N.122, T.124, N.125, V.127, E.154, F.157 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain B: N.331, P.579, Q.580, L.582 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain B: N.343, A.344, T.345, S.371 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: N.603, T.604 Ligand excluded by PLIP NAG.35: 7 residues within 4Å: Chain B: N.616, T.618, E.619, Q.644, T.645, R.646 Chain C: I.834 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.37: 6 residues within 4Å: Chain B: N.709, N.710, I.1130, G.1131 Chain C: I.794, D.796 Ligand excluded by PLIP NAG.38: 6 residues within 4Å: Chain B: A.706, A.713, E.1072, K.1073, N.1074 Chain C: Q.895 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain A: Y.351, I.468 Chain B: N.164, N.165 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain B: C.15, N.17, T.19, N.137 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.43: 6 residues within 4Å: Chain C: N.122, T.124, N.125, V.127, E.154, F.157 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain C: N.331, P.579, Q.580, L.582 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain C: N.343, A.344, T.345, S.371 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: N.603, T.604 Ligand excluded by PLIP NAG.48: 7 residues within 4Å: Chain A: I.834 Chain C: N.616, T.618, E.619, Q.644, T.645, R.646 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.50: 6 residues within 4Å: Chain A: I.794, D.796 Chain C: N.709, N.710, I.1130, G.1131 Ligand excluded by PLIP NAG.51: 6 residues within 4Å: Chain A: Q.895 Chain C: A.706, A.713, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain B: Y.351, I.468 Chain C: N.164, N.165 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain C: C.15, N.17, T.19, N.137 Ligand excluded by PLIP

3 x STE: STEARIC ACID(Non-covalent)

STE.28: 27 residues within 4Å: Chain A: C.336, P.337, F.338, V.341, F.342, I.358, A.363, Y.365, L.368, Y.369, S.373, F.374, F.377, L.387, F.392, V.395, A.397, C.432, I.434, L.513, F.515, V.524 Chain C: R.408, Q.409, T.415, G.416, K.417 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:F.338, A:F.338, A:I.358, A:A.363, A:Y.365, A:Y.365, A:L.368, A:Y.369, A:F.377, A:F.377, A:F.392, A:F.392, A:I.434 Salt bridges: C:R.408, C:K.417 STE.41: 27 residues within 4Å: Chain A: R.408, Q.409, T.415, G.416, K.417 Chain B: C.336, P.337, F.338, V.341, F.342, I.358, A.363, Y.365, L.368, Y.369, S.373, F.374, F.377, L.387, F.392, V.395, A.397, C.432, I.434, L.513, F.515, V.524 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.338, B:F.338, B:I.358, B:A.363, B:Y.365, B:Y.365, B:L.368, B:Y.369, B:F.377, B:F.377, B:F.392, B:F.392, B:V.395, B:I.434 Salt bridges: A:R.408, A:K.417 STE.54: 27 residues within 4Å: Chain B: R.408, Q.409, T.415, G.416, K.417 Chain C: C.336, P.337, F.338, V.341, F.342, I.358, A.363, Y.365, L.368, Y.369, S.373, F.374, F.377, L.387, F.392, V.395, A.397, C.432, I.434, L.513, F.515, V.524 15 PLIP interactions: 2 interactions with chain B, 13 interactions with chain C Salt bridges: B:R.408, B:K.417 Hydrophobic interactions: C:F.338, C:F.338, C:I.358, C:A.363, C:Y.365, C:Y.365, C:L.368, C:Y.369, C:F.377, C:F.377, C:F.392, C:F.392, C:I.434

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duyvesteyn, H.M.E. et al., The SARS-CoV-2 Spike harbours a lipid binding pocket which modulates stability of the prefusion trimer. bioRxiv (2020)

Release Date

2022-05-04

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein