SMTL ID : 9gxe.1

Structure of the SARS-CoV spike glycoprotein in complex with a homotrimeric Bicycle molecule

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

9 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: N.1085, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 1 residues within 4Å: Chain A: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.704, L.909, Q.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.704, L.909, Q.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain C: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: N.704, L.909, Q.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP)

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

NAG.10: 2 residues within 4Å: Chain A: N.696, G.1118 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: C.2, N.4, N.124 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain A: N.109, T.111, V.114, V.158 Ligand excluded by PLIP NAG.13: 8 residues within 4Å: Chain A: T.95, N.221, T.223 Chain C: R.444, S.446, N.447, K.449, E.452 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.330, S.358 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.603 Chain B: I.821 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.788, S.790 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: N.696, G.1118 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain B: N.1121 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: C.2, N.4, N.124 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: A.693, E.1059, N.1061 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.330, S.358 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.109, T.111, V.114 Ligand excluded by PLIP NAG.24: 6 residues within 4Å: Chain A: R.444, S.446, N.447, E.452 Chain B: T.95, N.221 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: N.603, T.605 Chain C: I.821 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: D.783 Chain C: N.696, G.1118 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: C.2, N.4, N.124 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain C: N.109, T.111, V.114, V.158 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: A.693, E.1059, N.1061 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.1121 Ligand excluded by PLIP NAG.32: 8 residues within 4Å: Chain B: R.444, S.446, N.447, L.448, E.452 Chain C: T.95, N.221, T.223 Ligand excluded by PLIP

3 x STE: STEARIC ACID(Non-covalent)

STE.17: 21 residues within 4Å: Chain A: R.395, Q.396, T.402, G.403 Chain B: C.323, P.324, F.325, V.328, F.329, I.345, A.350, Y.352, L.355, Y.356, F.361, F.364, L.374, F.379, V.382, L.500, F.502 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.325, B:V.328, B:F.329, B:I.345, B:A.350, B:Y.352, B:Y.352, B:L.355, B:F.361, B:F.361, B:F.364, B:F.364, B:L.374, B:L.374, B:F.379, B:L.500 Salt bridges: A:R.395 STE.26: 20 residues within 4Å: Chain B: R.395, Q.396, T.402, G.403 Chain C: C.323, P.324, F.325, I.345, A.350, Y.352, L.355, Y.356, F.361, F.364, L.374, F.379, V.382, I.421, L.500, F.502 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.325, C:F.325, C:I.345, C:A.350, C:Y.352, C:Y.352, C:L.355, C:Y.356, C:F.361, C:F.364, C:F.364, C:L.374, C:F.379, C:V.382, C:I.421, C:F.502 Salt bridges: B:R.395 STE.33: 19 residues within 4Å: Chain A: C.323, P.324, F.325, V.328, F.329, I.345, Y.352, Y.356, F.361, F.364, L.374, F.379, V.382, L.500, F.502 Chain C: R.395, Q.396, T.402, G.403 20 PLIP interactions: 17 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:F.325, A:V.328, A:F.329, A:Y.352, A:Y.352, A:Y.356, A:F.361, A:F.361, A:F.364, A:F.364, A:F.364, A:L.374, A:L.374, A:F.379, A:L.500, A:L.500, A:F.502 Hydrogen bonds: C:Q.396, C:T.402 Salt bridges: C:R.395

3 x KZ0: 2,4,6-tris(chloromethyl)-1,3,5-triazine(Covalent)

KZ0.34: 8 residues within 4Å: Chain A: Y.436, S.481 Chain D: C.2, P.3, T.10, C.11, C.14, A.15 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.436, A:Y.436 pi-Stacking: A:Y.436 KZ0.35: 8 residues within 4Å: Chain B: Y.436, S.481 Chain E: C.2, P.3, T.10, C.11, C.14, A.15 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.436, B:Y.436 pi-Stacking: B:Y.436 KZ0.36: 7 residues within 4Å: Chain C: Y.436, S.481 Chain F: C.2, T.10, C.11, C.14, A.15 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.436, C:Y.436 pi-Stacking: C:Y.436

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Drulyte, I. et al., Structure of the SARS-CoV spike glycoprotein in complex with a homotrimeric Bicycle molecule. To Be Published

Release Date

2025-03-26

Peptides

Spike glycoprotein: ABC
Homotrimeric bicycle molecule: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Spike glycoprotein

Homotrimeric bicycle molecule

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