SMTL ID : 9b4x.1

SARS CoV-2 full-length spike protein with Lys1269Ala and His1271Ala substitutions in the coatomer binding motif, 1RBD-up conformation (SPIKE-AXA)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

12 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.1: 2 residues within 4Å: Chain A: Y.67, N.100 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain A: V.159, N.160, N.161, A.162, V.166, K.168 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.168 NAG-NAG.3: 4 residues within 4Å: Chain A: T.147, T.148, N.273, T.275 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: G.378, E.379, F.381, N.382 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain A: N.655, C.656, T.657, Q.683 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain A: N.756, F.757, T.758, L.961, A.1109 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain B: N.748, N.749, I.1169, G.1170 Chain C: D.835 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain B: N.655, T.657 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain C: G.378, E.379, N.382, S.412 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain A: D.835 Chain C: N.748, I.1169, G.1170 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain C: S.151, E.171, N.203, N.204 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 4 residues within 4Å: Chain C: N.655, C.656, T.657, Q.683 No protein-ligand interaction detected (PLIP)

16 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: 3 residues within 4Å: Chain A: N.319, E.320, N.321 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 2 residues within 4Å: Chain A: V.1172, N.1173 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 5 residues within 4Å: Chain A: N.370, T.372, Q.619, T.620, L.621 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 5 residues within 4Å: Chain A: N.840, F.841, S.842, Q.843, I.970 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.842 NAG-NAG-BMA.11: 4 residues within 4Å: Chain A: A.745, S.750, N.1113 Chain B: Q.934 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 4 residues within 4Å: Chain A: N.748, N.749, G.1170 Chain B: D.835 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 3 residues within 4Å: Chain A: K.597 Chain B: E.320, N.321 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 3 residues within 4Å: Chain B: N.756, T.758, L.961 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 4 residues within 4Å: Chain B: N.1137, T.1139, H.1140, F.1142 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 2 residues within 4Å: Chain B: V.1172, N.1173 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 6 residues within 4Å: Chain B: F.377, G.378, F.381, N.382, D.403, V.406 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.26: 4 residues within 4Å: Chain C: T.147, N.273, I.274, T.275 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 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.29: 6 residues within 4Å: Chain C: 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 NAG-NAG-BMA.30: 3 residues within 4Å: Chain C: N.840, S.842, Q.843 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.32: 4 residues within 4Å: Chain C: N.1137, T.1139, H.1140, F.1142 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- NAG- FUC: alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]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-NAG-FUC.12: 4 residues within 4Å: Chain A: N.1137, T.1139, H.1140, F.1142 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.18: 4 residues within 4Å: Chain B: N.840, S.842, Q.843, Q.974 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.20: 5 residues within 4Å: Chain B: A.745, E.1111, K.1112, N.1113 Chain C: Q.934 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.1113 NAG-NAG-FUC.31: 2 residues within 4Å: Chain A: Q.934 Chain C: N.1113 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.934, A:Q.934

1 x NAG- NAG- BMA- MAN- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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-NAG.33: 1 residues within 4Å: Chain C: N.1173 No protein-ligand interaction detected (PLIP)

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

NAG.34: 7 residues within 4Å: Chain A: S.151, K.152, T.153, E.171, N.203, N.204 Ligands: NAG.37 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: T.346, T.641, N.642 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain A: F.682, H.694, N.696 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Ligands: NAG.34 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: 7 residues within 4Å: Chain B: K.186, N.187, N.188, S.190, M.192, S.295, G.296 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain B: G.271, I.272, N.273 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain B: N.370, Q.619 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain B: E.348, G.640, N.642, T.643 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain B: H.694, V.695, N.696 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain A: R.396 Chain B: N.204, C.205, T.206 Ligand excluded by PLIP NAG.45: 7 residues within 4Å: Chain B: V.159, N.161, T.163, N.164, V.166, F.196, Y.199 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: Y.67, N.100 Ligand excluded by PLIP NAG.47: 5 residues within 4Å: Chain C: Y.183, N.188, S.190, S.194, E.195 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain C: N.370, T.372, Q.619, T.620 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain C: H.694, N.696 Ligand excluded by PLIP NAG.50: 13 residues within 4Å: Chain C: E.135, N.138, I.139, I.140, R.141, N.160, N.161, W.191, M.192, E.193, L.218, R.229, A.282 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain C: N.642 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, S. et al., Cryo-EM structure of SARS CoV-2 full-length spike with Lys1269Ala and His1271Ala substitutions 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

Related Entries With Identical Sequence