SMTL ID : 9b8f.1

SARS CoV-2 full-length spike protein with Lys1269Ala and His1271Ala substitutions in the coatomer binding motif, 2RBD-up conformation (SPIKE-AXA)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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.1: 4 residues within 4Å: Chain B: N.319, E.320, N.321, T.323 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 4 residues within 4Å: Chain A: N.1137, T.1139, H.1140, F.1142 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 5 residues within 4Å: Chain A: C.1121, C.1165, I.1171, V.1172, N.1173 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 5 residues within 4Å: Chain A: K.834, N.840, F.841, S.842, L.845 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 5 residues within 4Å: Chain B: N.748, N.749, G.1170 Chain C: I.833, D.835 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 6 residues within 4Å: Chain B: N.655, C.656, T.657, E.658, Q.683 Chain C: Q.875 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.875 NAG-NAG-BMA.16: 8 residues within 4Å: Chain B: T.755, N.756, F.757, T.758, N.958, L.961, Q.1110, F.1148 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 3 residues within 4Å: Chain B: I.1171, V.1172, N.1173 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 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.20: 8 residues within 4Å: Chain C: G.378, E.379, N.382, V.406, L.407, S.410, S.412, F.413 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.412 NAG-NAG-BMA.21: 4 residues within 4Å: Chain B: K.597 Chain C: N.319, E.320, N.321 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.25: 5 residues within 4Å: Chain A: Q.934 Chain C: A.745, A.752, E.1111, N.1113 No protein-ligand interaction detected (PLIP)

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.2: 4 residues within 4Å: Chain B: K.834, N.840, S.842, Q.843 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.3: 9 residues within 4Å: Chain B: K.1112, F.1114, V.1135, S.1136, N.1137, T.1139, H.1140, F.1142, Y.1149 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:H.1140, B:F.1142 Hydrogen bonds: B:T.1139, B:H.1140, B:H.1140, B:H.1140

8 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.4: 4 residues within 4Å: Chain A: N.319, E.320, N.321, T.323 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: N.655, T.657, Q.683 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain A: A.745, S.750, E.1111, K.1112, N.1113 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain A: Y.746, S.747, N.748, N.749 Chain B: I.833, D.835 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 8 residues within 4Å: Chain B: N.161, A.162, T.163, N.164, V.165, V.166, F.196, V.210 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 5 residues within 4Å: Chain B: A.745, S.750, N.1113, F.1114, T.1115 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 3 residues within 4Å: Chain A: I.833, D.835 Chain C: N.748 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 5 residues within 4Å: Chain C: S.151, K.152, E.171, N.203, N.204 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-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.5: 4 residues within 4Å: Chain A: R.367, N.370, Q.619, T.620 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.619, A:T.620 Hydrogen bonds: A:N.370

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.7: 8 residues within 4Å: Chain A: N.756, F.757, T.758, L.961, N.964, Q.965, A.1109, Q.1110 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.961, A:Q.965 Hydrogen bonds: A:Q.965 NAG-NAG-BMA-MAN.23: 9 residues within 4Å: Chain C: T.755, N.756, F.757, T.758, N.958, L.961, Q.965, Q.1110, F.1148 No protein-ligand interaction detected (PLIP)

1 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.22: 8 residues within 4Å: Chain A: I.873, K.874, Q.875 Chain C: N.655, C.656, T.657, E.658, Q.683 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:K.874, A:K.874, C:N.655

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.24: 5 residues within 4Å: Chain C: K.834, G.838, N.840, S.842, Q.843 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.27: 5 residues within 4Å: Chain C: C.1121, G.1124, I.1171, V.1172, N.1173 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-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.26: 8 residues within 4Å: Chain C: V.1135, S.1136, N.1137, G.1138, T.1139, H.1140, W.1141, F.1142 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.1140, C:T.1139, C:T.1139, C:H.1140 Hydrophobic interactions: C:T.1139

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

NAG.30: 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.31: 1 residues within 4Å: Chain A: N.642 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain A: E.693, H.694, V.695, N.696 Ligand excluded by PLIP NAG.33: 5 residues within 4Å: Chain A: Y.67, T.68, N.69, F.98, N.100 Ligand excluded by PLIP NAG.34: 8 residues within 4Å: Chain A: G.181, V.182, Y.183, N.188, S.190, W.191, M.192, S.194 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain A: E.171, N.203, N.204, C.205 Chain C: R.505 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: Y.67, N.69, N.100 Ligand excluded by PLIP NAG.37: 7 residues within 4Å: Chain B: F.368, P.369, N.370, I.371, T.372, Q.619, T.620 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: N.642, T.643 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: H.694, N.696 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain B: G.378, F.381, N.382, L.407, F.413 Ligand excluded by PLIP NAG.41: 6 residues within 4Å: Chain B: H.185, K.186, N.187, N.188, K.189, W.297 Ligand excluded by PLIP NAG.42: 6 residues within 4Å: Chain A: R.396 Chain B: Q.154, E.171, N.204, C.205, T.206 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: F.98, S.99, N.100 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: T.346, N.642 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: H.694, N.696 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.188 Ligand excluded by PLIP NAG.47: 5 residues within 4Å: Chain C: T.147, T.148, T.153, N.273, T.275 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 Lys1269Ala and His1271Ala substitutions 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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