SMTL ID : 9bbk.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

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: 2 residues within 4Å: Chain A: N.655, T.657 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain A: N.319, E.320, N.321 Chain C: K.597 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 8 residues within 4Å: Chain B: V.159, N.161, T.163, N.164, V.166, F.196, V.198, Y.199 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.196, B:V.198, B:Y.199 Hydrogen bonds: B:Y.199 NAG-NAG.11: 3 residues within 4Å: Chain A: K.597 Chain B: E.320, N.321 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain B: N.748, I.1169, G.1170 Chain C: D.835 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain C: T.147, N.273, T.275 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain C: N.319, E.320, N.321 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 11 residues within 4Å: Chain C: G.378, E.379, F.381, N.382, L.407, S.410, S.412, F.413, W.475, L.480, R.548 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 4 residues within 4Å: Chain A: D.835 Chain C: N.748, I.1169, G.1170 No protein-ligand interaction detected (PLIP)

11 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: 4 residues within 4Å: Chain A: N.370, P.618, Q.619, T.620 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.619, A:T.620 NAG-NAG-BMA.3: 6 residues within 4Å: Chain A: N.756, T.758, L.961, N.964, Q.965, Q.1110 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.964 NAG-NAG-BMA.4: 4 residues within 4Å: Chain A: N.840, S.842, Q.843, Q.974 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 4 residues within 4Å: Chain A: N.1137, T.1139, H.1140, F.1142 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 3 residues within 4Å: Chain A: I.1171, V.1172, N.1173 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 5 residues within 4Å: Chain A: N.748, I.1169, G.1170 Chain B: I.833, D.835 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 1 residues within 4Å: Chain B: N.1173 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 8 residues within 4Å: Chain B: F.377, G.378, F.381, N.382, V.406, L.407, N.409, S.410 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 3 residues within 4Å: Chain C: N.370, Q.619, T.620 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.620, C:T.620 NAG-NAG-BMA.20: 2 residues within 4Å: Chain C: N.655, T.657 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 4 residues within 4Å: Chain C: C.1121, I.1171, V.1172, N.1173 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.5: 6 residues within 4Å: Chain A: S.743, V.744, A.745, E.1111, N.1113 Chain B: Q.934 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.745 Hydrogen bonds: A:S.743, A:N.1113 NAG-NAG-FUC.25: 4 residues within 4Å: Chain A: Q.934 Chain C: A.745, E.1111, N.1113 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.1113

2 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.12: 6 residues within 4Å: Chain B: N.756, T.758, L.961, N.964, Q.965, Q.1110 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.964 NAG-NAG-BMA-MAN.13: 3 residues within 4Å: Chain B: N.840, S.842, Q.843 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.14: 6 residues within 4Å: Chain B: S.743, A.745, S.750, N.1113, T.1115 Chain C: Q.934 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.745 Hydrogen bonds: B:S.750, B:N.1113

3 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: 4 residues within 4Å: Chain B: N.1137, T.1139, H.1140, F.1142 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.23: 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 Hydrophobic interactions: C:N.964 NAG-NAG-BMA-MAN.24: 2 residues within 4Å: Chain C: N.840, S.842 No protein-ligand interaction detected (PLIP)

1 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.26: 4 residues within 4Å: Chain C: N.1137, T.1139, H.1140, F.1142 No protein-ligand interaction detected (PLIP)

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

NAG.30: 8 residues within 4Å: Chain A: N.161, T.163, N.164, V.166, K.168, F.196, Y.199, V.210 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: G.271, I.272, N.273 Ligand excluded by PLIP NAG.32: 10 residues within 4Å: Chain A: H.108, V.182, Y.183, Y.184, H.185, N.188, S.190, W.191, L.283, A.301 Ligand excluded by PLIP NAG.33: 7 residues within 4Å: Chain A: T.153, Q.154, E.171, N.204, T.206 Chain C: R.394, R.505 Ligand excluded by PLIP NAG.34: 7 residues within 4Å: Chain A: F.381, N.382, S.410, A.411, S.412, W.475, L.480 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain A: G.640, N.642 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain A: N.696, N.697 Ligand excluded by PLIP NAG.37: 13 residues within 4Å: Chain A: N.69, S.70, F.71, T.72, R.73, L.95, P.96, F.97, F.98, S.99, N.100, V.101, Y.130 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: Y.67, N.100 Ligand excluded by PLIP NAG.39: 6 residues within 4Å: Chain B: Y.183, K.186, N.187, N.188, M.192, S.194 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain A: R.396 Chain B: N.204 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: G.238, G.271, N.273 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain B: N.696 Ligand excluded by PLIP NAG.43: 6 residues within 4Å: Chain B: F.368, P.369, N.370, P.618, Q.619, T.620 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain B: G.640, N.642, T.643 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain B: N.655, T.657, Q.683 Chain C: I.873 Ligand excluded by PLIP NAG.46: 8 residues within 4Å: Chain C: N.161, A.162, T.163, V.166, M.192, E.193, F.196, Y.199 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: Y.67, N.100 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: N.203, N.204 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain C: G.640, N.642, T.643 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: H.694, N.696 Ligand excluded by PLIP

Links

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Citation

Singh, S. et al., Structure of SARS CoV-2 full-length spike protein with His1271Lys substitution in the coatomer binding motif, 2RBD-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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