SMTL ID : 9bea.1

Structure of SARS-CoV-2 full-length WT spike protein with internal tag, 2RBD-up conformation (SPIKE-WT)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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.1: 4 residues within 4Å: Chain A: N.655, C.656, T.657, Q.683 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.657 NAG-NAG-BMA.4: 4 residues within 4Å: Chain A: N.370, P.618, Q.619, T.620 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 7 residues within 4Å: Chain A: K.834, F.836, F.839, N.840, F.841, S.842, Q.843 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.843 NAG-NAG-BMA.10: 3 residues within 4Å: Chain A: I.1171, V.1172, N.1173 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 5 residues within 4Å: Chain B: N.655, T.657, E.658 Chain C: I.873, Q.875 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 3 residues within 4Å: Chain B: N.840, S.842, Q.843 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 3 residues within 4Å: Chain C: H.694, V.695, N.696 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 4 residues within 4Å: Chain A: D.835 Chain C: N.748, I.1169, G.1170 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 3 residues within 4Å: Chain C: T.147, N.273, T.275 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.29: 5 residues within 4Å: Chain A: I.873, Q.875 Chain C: N.655, T.657, Q.683 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 3 residues within 4Å: Chain C: N.840, S.842, Q.843 No protein-ligand interaction detected (PLIP)

7 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 5 residues within 4Å: Chain B: S.747, N.748, I.1169, G.1170 Chain C: D.835 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 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.11: 3 residues within 4Å: Chain B: H.694, V.695, N.696 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain B: N.161, T.163, N.164, V.166, F.196 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain C: Y.67, N.69, F.98, S.99, N.100 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain C: E.171, N.203, N.204 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 9 residues within 4Å: Chain C: G.378, E.379, F.381, N.382, V.406, L.407, S.410, S.412, F.413 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.410

6 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.5: 8 residues within 4Å: Chain A: F.82, N.319, E.320, N.321, G.322, T.323 Chain C: K.597, L.599 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.12: 9 residues within 4Å: Chain B: F.377, G.378, F.381, N.382, V.406, L.407, S.410, S.412, F.413 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.14: 3 residues within 4Å: Chain B: E.320, N.321, T.323 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.16: 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:Q.965 NAG-NAG-BMA-MAN.24: 5 residues within 4Å: Chain C: P.369, N.370, P.618, Q.619, T.620 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.32: 4 residues within 4Å: Chain C: N.1137, T.1139, H.1140, F.1142 No protein-ligand interaction detected (PLIP)

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.6: 6 residues within 4Å: Chain A: N.756, T.758, L.961, N.964, Q.965, Q.1110 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.961, A:N.964, A:Q.965 NAG-NAG-BMA-MAN-MAN.9: 7 residues within 4Å: Chain A: S.1136, N.1137, G.1138, T.1139, H.1140, W.1141, F.1142 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.8: 7 residues within 4Å: Chain A: V.744, A.745, A.752, E.1111, N.1113, F.1114, T.1115 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1113 NAG-NAG-FUC.18: 7 residues within 4Å: Chain B: S.743, V.744, A.745, A.752, E.1111, K.1112, N.1113 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.1113

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

NAG-NAG-MAN-MAN.19: 5 residues within 4Å: Chain B: N.1137, G.1138, T.1139, H.1140, F.1142 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.1140

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

NAG-NAG-MAN-MAN.20: 2 residues within 4Å: Chain B: C.1165, N.1173 No protein-ligand interaction detected (PLIP)

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

NAG-BMA.28: 2 residues within 4Å: Chain C: E.320 Ligands: NAG.49 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:E.320

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.31: 7 residues within 4Å: Chain C: T.755, N.756, L.961, N.964, Q.965, Q.1110, F.1148 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.961, C:N.964

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.33: 7 residues within 4Å: Chain A: Q.934 Chain C: A.745, S.750, A.752, E.1111, N.1113, T.1115 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.1115

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.34: 2 residues within 4Å: Chain C: C.1121, N.1173 No protein-ligand interaction detected (PLIP)

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

NAG.35: 6 residues within 4Å: Chain A: N.161, A.162, T.163, V.166, K.168, V.210 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain A: T.147, N.273 Ligand excluded by PLIP NAG.37: 6 residues within 4Å: Chain A: E.348, K.349, G.640, T.641, N.642, T.643 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain A: H.694, N.696 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain A: K.152, T.153, E.171, N.203, N.204 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain A: N.382, A.383, T.384 Ligand excluded by PLIP NAG.41: 5 residues within 4Å: Chain B: Y.183, K.186, N.187, N.188, M.192 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain B: N.370, P.618, Q.619, T.620 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain B: K.349, G.640, N.642, T.643 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain B: E.171, N.204 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain B: Y.67, T.68, N.69, N.100 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain B: T.147, N.273, T.275 Ligand excluded by PLIP NAG.47: 7 residues within 4Å: Chain C: V.182, Y.183, N.188, S.190, M.192, S.194, E.195 Ligand excluded by PLIP NAG.48: 6 residues within 4Å: Chain C: T.346, V.347, E.348, T.641, N.642, T.643 Ligand excluded by PLIP NAG.49: 5 residues within 4Å: Chain B: K.597 Chain C: N.319, E.320, N.321 Ligands: NAG-BMA.28 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, S. et al., Structure of SARS CoV-2 full-length spike protein with internal tag, 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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