SMTL ID : 9b9u.1

SARS-CoV-2 full-length spike protein with His1271Lys substitution in the coatomer binding motif, 1RBD-up conformation (SPIKE-KXK)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

10 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: 5 residues within 4Å: Chain A: T.147, N.273, T.275 Chain C: R.496, K.501 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: N.382, V.406, N.409, S.410, S.412 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.406 NAG-NAG.5: 7 residues within 4Å: Chain A: V.654, N.655, C.656, T.657, Q.683 Chain B: A.885, R.886 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:R.886 NAG-NAG.10: 4 residues within 4Å: Chain A: N.748, I.1169, G.1170 Chain B: D.835 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain A: Y.67, T.68, N.69, N.100 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.67, A:N.100 Hydrogen bonds: A:N.100 NAG-NAG.14: 4 residues within 4Å: Chain B: N.655, C.656, T.657, Q.683 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.657 NAG-NAG.18: 4 residues within 4Å: Chain B: N.748, N.749, G.1170 Chain C: D.835 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 8 residues within 4Å: Chain B: N.161, T.163, N.164, V.165, V.166, K.168, Y.199, V.210 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.166, B:Y.199 Hydrogen bonds: B:K.168 NAG-NAG.24: 5 residues within 4Å: Chain C: N.655, C.656, T.657, E.658, Q.683 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 5 residues within 4Å: Chain C: S.151, K.152, A.202, N.203, N.204 No protein-ligand interaction detected (PLIP)

12 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 5 residues within 4Å: Chain A: N.319, E.320, N.321, T.323 Chain C: K.597 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 3 residues within 4Å: Chain A: I.1171, V.1172, N.1173 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 5 residues within 4Å: Chain A: P.369, N.370, P.618, Q.619, T.620 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 5 residues within 4Å: Chain A: N.756, T.758, L.961, Q.965, Q.1110 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 3 residues within 4Å: Chain A: K.597 Chain B: E.320, N.321 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 4 residues within 4Å: Chain B: G.378, F.381, N.382, V.406 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 3 residues within 4Å: Chain B: K.597 Chain C: E.320, N.321 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.25: 11 residues within 4Å: Chain B: F.525, N.526, Y.528 Chain C: F.377, G.378, F.381, N.382, V.406, L.407, S.410, F.413 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.406 NAG-NAG-BMA.26: 4 residues within 4Å: Chain A: I.833, D.835 Chain C: N.748, N.749 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 3 residues within 4Å: Chain C: I.1171, V.1172, N.1173 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.29: 4 residues within 4Å: Chain C: T.147, T.148, N.273, T.275 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 7 residues within 4Å: Chain C: N.756, F.757, T.758, L.961, N.964, Q.965, Q.1110 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.964

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.8: 3 residues within 4Å: Chain A: N.840, S.842, Q.843 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.16: 5 residues within 4Å: Chain B: N.1137, G.1138, T.1139, H.1140, F.1142 No protein-ligand interaction detected (PLIP)

1 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.9: 9 residues within 4Å: Chain A: A.745, S.750, A.752, E.1111, N.1113, F.1114 Chain B: A.932, L.933, Q.934 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-3)-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-MAN-FUC.12: 5 residues within 4Å: Chain A: N.1137, T.1139, F.1142, Y.1149, I.1153 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.1139 Hydrogen bonds: A:N.1137, A:Y.1149, A:Y.1149 NAG-NAG-BMA-MAN-FUC.33: 5 residues within 4Å: Chain C: N.1137, T.1139, H.1140, F.1142, I.1153 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.15: 5 residues within 4Å: Chain B: N.756, T.758, L.961, Q.965, Q.1110 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.961 NAG-NAG-BMA-MAN.31: 4 residues within 4Å: Chain C: N.840, S.842, Q.843, Q.974 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.20: 3 residues within 4Å: Chain B: N.840, S.842, Q.843 No protein-ligand interaction detected (PLIP)

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.21: 7 residues within 4Å: Chain B: S.743, V.744, A.745, E.1111, K.1112, N.1113 Chain C: Q.934 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.1113 NAG-NAG-FUC.32: 10 residues within 4Å: Chain A: L.933, Q.934 Chain C: S.743, V.744, A.745, S.750, A.752, E.1111, K.1112, N.1113 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Q.934, C:N.1113

1 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN-FUC.22: 5 residues within 4Å: Chain B: C.1121, C.1165, I.1171, V.1172, N.1173 No protein-ligand interaction detected (PLIP)

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

NAG.34: 2 residues within 4Å: Chain A: H.694, N.696 Ligand excluded by PLIP NAG.35: 7 residues within 4Å: Chain A: N.161, A.162, T.163, N.164, V.166, K.168, V.210 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain A: N.203, N.204 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain A: K.349, G.640, N.642, T.643 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain B: Y.67, N.69, F.98, S.99, N.100 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: G.271, I.272, N.273 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: N.642, T.643 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: H.694, V.695, N.696 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain B: E.171, N.203, N.204 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain B: N.370, Q.619 Ligand excluded by PLIP NAG.44: 9 residues within 4Å: Chain B: Y.183, Y.184, H.185, K.186, N.187, N.188, S.190, W.191, M.192 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: Y.67, S.99, N.100 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: N.188, K.189, S.190 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.696 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: N.642, T.643 Ligand excluded by PLIP NAG.49: 7 residues within 4Å: Chain C: V.159, N.161, T.163, N.164, V.166, E.193, Y.199 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: N.370, Q.619 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, S. et al., SARS CoV-2 full-length spike protein with His1271Lys substitution in the coatomer binding motif, 1RBD-up conformation. To Be Published

Release Date

2025-04-16

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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