SMTL ID : 9bd9.1

SARS CoV-2 full-length WT spike protein, 1RBD-up conformation (SPIKE-WT)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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.1: 4 residues within 4Å: Chain A: N.319, E.320, N.321 Chain C: K.597 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.8: 3 residues within 4Å: Chain A: N.840, S.842, Q.843 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.28: 4 residues within 4Å: Chain B: K.597 Chain C: N.319, E.320, N.321 No protein-ligand interaction detected (PLIP)

12 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: 3 residues within 4Å: Chain A: H.694, V.695, N.696 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: N.748, N.749, A.1117, P.1118, G.1170 Chain B: D.835 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.748, A:N.749 NAG-NAG.6: 6 residues within 4Å: Chain A: N.655, T.657, Q.683 Chain B: A.885, R.886, D.887 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain B: T.147, T.148, N.273, T.275 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain B: N.748, I.1169, G.1170 Chain C: D.835 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 7 residues within 4Å: Chain A: Y.435, H.558 Chain B: Q.154, E.171, N.204, C.205, T.206 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 7 residues within 4Å: Chain B: N.161, A.162, T.163, N.164, V.166, V.210, P.213 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 6 residues within 4Å: Chain B: Y.528 Chain C: G.378, E.379, N.382, S.410, S.412 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 5 residues within 4Å: Chain A: D.835 Chain C: N.748, N.749, I.1169, G.1170 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain C: K.152, E.171, N.203, N.204 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 5 residues within 4Å: Chain C: T.147, T.148, N.273, T.275, R.276 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 3 residues within 4Å: Chain A: K.874 Chain C: N.655, T.657 No protein-ligand interaction detected (PLIP)

8 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.4: 9 residues within 4Å: Chain A: F.377, G.378, F.381, N.382, V.406, S.410, A.411, S.412, F.413 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.406, A:A.411, A:S.412 NAG-NAG-BMA.5: 7 residues within 4Å: Chain A: R.367, P.369, N.370, P.618, Q.619, T.620, L.621 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.619, A:T.620 NAG-NAG-BMA.7: 7 residues within 4Å: Chain A: T.755, N.756, T.758, L.961, N.964, Q.965, Q.1110 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.961, A:N.964, A:Q.965 Hydrogen bonds: A:N.964 NAG-NAG-BMA.11: 3 residues within 4Å: Chain A: I.1171, V.1172, N.1173 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 4 residues within 4Å: Chain B: G.378, N.382, S.410, S.412 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 3 residues within 4Å: Chain A: K.597 Chain B: E.320, N.321 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 5 residues within 4Å: Chain B: N.655, T.657, E.658, Q.683 Chain C: I.873 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 7 residues within 4Å: Chain C: T.755, N.756, T.758, L.961, N.964, Q.965, Q.1110 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.961

3 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.9: 8 residues within 4Å: Chain A: A.745, S.750, N.1113, F.1114, T.1115, S.1136, N.1137 Chain B: Q.934 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.1115, A:T.1115, A:S.1136 NAG-NAG-FUC.21: 6 residues within 4Å: Chain B: S.743, V.744, A.745, S.750, N.1113 Chain C: Q.934 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.1113 NAG-NAG-FUC.32: 6 residues within 4Å: Chain A: Q.934 Chain C: S.743, A.745, S.750, E.1111, N.1113 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[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-MAN.10: 5 residues within 4Å: Chain A: N.1137, G.1138, T.1139, H.1140, F.1142 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.1140

4 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.19: 5 residues within 4Å: Chain B: N.756, L.961, N.964, Q.965, Q.1110 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.961 NAG-NAG-BMA-MAN.20: 4 residues within 4Å: Chain B: N.840, S.842, Q.843, Q.974 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.31: 3 residues within 4Å: Chain C: N.840, S.842, Q.843 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.33: 5 residues within 4Å: Chain C: N.1137, G.1138, T.1139, H.1140, F.1142 No protein-ligand interaction detected (PLIP)

1 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.22: 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- 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.23: 1 residues within 4Å: Chain B: N.1173 No protein-ligand interaction detected (PLIP)

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

NAG-FUC.34: 7 residues within 4Å: Chain C: C.1121, C.1165, I.1171, V.1172, N.1173 Ligands: NAG-BMA.35, NAG-BMA.35 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.1171, C:N.1173

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

NAG-BMA.35: 3 residues within 4Å: Chain C: D.1166 Ligands: NAG-FUC.34, NAG-FUC.34 No protein-ligand interaction detected (PLIP)

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

NAG.36: 5 residues within 4Å: Chain A: Y.67, N.69, F.98, S.99, N.100 Ligand excluded by PLIP NAG.37: 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.38: 2 residues within 4Å: Chain A: N.203, N.204 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain A: T.147, T.148, N.273, T.275 Ligands: NAG.41 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain A: N.642, T.643 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain A: R.276 Ligands: NAG.39 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: Y.67, N.100 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain B: Y.183, K.186, N.187, N.188, M.192 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain B: N.370, I.371, T.372, Q.619, T.620 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain B: N.642 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain B: H.694, V.695, N.696 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain C: Y.67, F.98, N.100 Ligand excluded by PLIP NAG.48: 5 residues within 4Å: Chain C: Y.183, N.188, S.190, S.194, E.195 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain C: N.642 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: H.694, N.696 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain C: N.370, I.371 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, 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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