SMTL ID : 6zp2.1

Structure of SARS-CoV-2 Spike Protein Trimer (K986P, V987P, single Arg S1/S2 cleavage site) in Locked State

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)(Non-covalent)

NAG-NAG.1: 3 residues within 4Å: Chain A: N.708, L.913, Q.917 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.913 NAG-NAG.2: 3 residues within 4Å: Chain A: N.792, S.794, Q.795 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.1125 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 8 residues within 4Å: Chain A: T.99, N.225, T.227 Chain B: R.448, K.449, S.450, N.451, E.456 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.113, T.115, N.116, V.162 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.708, L.913, Q.917 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.913 NAG-NAG.7: 3 residues within 4Å: Chain B: N.792, S.794, Q.795 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.1125 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 8 residues within 4Å: Chain B: T.99, N.225, T.227 Chain C: R.448, K.449, S.450, N.451, E.456 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain B: N.113, T.115, N.116, V.162 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: N.708, L.913, Q.917 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.913 NAG-NAG.12: 3 residues within 4Å: Chain C: N.792, S.794, Q.795 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain C: N.1125 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 8 residues within 4Å: Chain A: R.448, K.449, S.450, N.451, E.456 Chain C: T.99, N.225, T.227 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain C: N.113, T.115, N.116, V.162 No protein-ligand interaction detected (PLIP)

3 x BLA: BILIVERDINE IX ALPHA(Non-covalent)

BLA.16: 11 residues within 4Å: Chain A: N.90, I.92, R.93, W.95, I.110, N.112, V.117, M.168, R.181, F.183, L.217 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:N.90, A:R.93, A:W.95, A:I.110, A:N.112, A:V.117, A:F.183, A:L.217, A:L.217 Hydrogen bonds: A:N.112 pi-Cation interactions: A:R.181 BLA.32: 11 residues within 4Å: Chain B: N.90, I.92, R.93, W.95, I.110, N.112, V.117, M.168, R.181, F.183, L.217 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:N.90, B:R.93, B:W.95, B:I.110, B:N.112, B:V.117, B:F.183, B:L.217, B:L.217 Hydrogen bonds: B:N.112 pi-Cation interactions: B:R.181 BLA.47: 11 residues within 4Å: Chain C: N.90, I.92, R.93, W.95, I.110, N.112, V.117, M.168, R.181, F.183, L.217 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:N.90, C:R.93, C:W.95, C:I.110, C:N.112, C:V.117, C:F.183, C:L.217, C:L.217 Hydrogen bonds: C:N.112 pi-Cation interactions: C:R.181

39 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.17: 2 residues within 4Å: Chain A: N.322, Q.571 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: E.300, N.594 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.607, T.609 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.648 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.700 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain A: A.697, E.1063, K.1064, N.1065 Chain C: Q.886 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: N.1089, T.1091, H.1092, F.1094 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: N.156 Chain B: Y.342 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: N.271, E.272, N.273 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: G.330, N.334, S.362 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: N.8, N.128 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain A: Y.19, N.52 Ligand excluded by PLIP NAG.30: 6 residues within 4Å: Chain A: H.137, N.139, N.140, S.142, W.143, M.144 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.322, Q.571 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: E.300, N.594 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: N.607, T.609 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.648 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain B: N.700 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain A: Q.886 Chain B: A.697, E.1063, K.1064, N.1065 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain B: N.1089, T.1091, H.1092, F.1094 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: N.156 Chain C: Y.342 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: N.271, E.272, N.273 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain B: G.330, N.334, S.362 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain B: N.8, N.128 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain B: Y.19, N.52 Ligand excluded by PLIP NAG.46: 6 residues within 4Å: Chain B: H.137, N.139, N.140, S.142, W.143, M.144 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: N.322, Q.571 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain C: E.300, N.594 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: N.607, T.609 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain C: N.648 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain C: N.700 Ligand excluded by PLIP NAG.53: 5 residues within 4Å: Chain B: Q.886 Chain C: A.697, E.1063, K.1064, N.1065 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain C: N.1089, T.1091, H.1092, F.1094 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain A: Y.342 Chain C: N.156 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain C: N.271, E.272, N.273 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain C: G.330, N.334, S.362 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain C: N.8, N.128 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain C: Y.19, N.52 Ligand excluded by PLIP NAG.60: 6 residues within 4Å: Chain C: H.137, N.139, N.140, S.142, W.143, M.144 Ligand excluded by PLIP

3 x EIC: LINOLEIC ACID(Non-covalent)

EIC.27: 17 residues within 4Å: Chain A: P.328, F.329, V.332, I.349, Y.356, L.359, Y.360, F.365, F.368, F.383, I.425, L.504, F.506 Chain B: R.399, Q.400, T.406, G.407 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.329, A:F.329, A:V.332, A:I.349, A:Y.356, A:Y.356, A:L.359, A:Y.360, A:F.365, A:F.365, A:F.368, A:F.368, A:F.383, A:I.425, A:L.504, A:F.506 Hydrogen bonds: B:Q.400 Salt bridges: B:R.399 EIC.31: 17 residues within 4Å: Chain A: R.399, Q.400, T.406, G.407 Chain C: P.328, F.329, V.332, I.349, Y.356, L.359, Y.360, F.365, F.368, F.383, I.425, L.504, F.506 18 PLIP interactions: 16 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.329, C:F.329, C:V.332, C:I.349, C:Y.356, C:Y.356, C:L.359, C:Y.360, C:F.365, C:F.365, C:F.368, C:F.368, C:F.383, C:I.425, C:L.504, C:F.506 Hydrogen bonds: A:Q.400 Salt bridges: A:R.399 EIC.43: 16 residues within 4Å: Chain B: P.328, F.329, V.332, I.349, Y.356, L.359, Y.360, F.365, F.368, F.383, I.425, L.504, F.506 Chain C: R.399, T.406, G.407 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:F.329, B:F.329, B:V.332, B:I.349, B:Y.356, B:Y.356, B:L.359, B:Y.360, B:F.365, B:F.365, B:F.368, B:F.368, B:F.383, B:I.425, B:L.504, B:F.506 Hydrogen bonds: C:Q.400 Salt bridges: C:R.399

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiong, X. et al., A thermostable, closed SARS-CoV-2 spike protein trimer. Nat.Struct.Mol.Biol. (2020)

Release Date

2020-07-22

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein