SMTL ID : 8g71.1

Spike/Nb2 complex with 1 RBD up

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

11 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: 4 residues within 4Å: Chain A: N.704, L.909, Q.913, Q.1058 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.909 NAG-NAG.2: 3 residues within 4Å: Chain A: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain B: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain C: N.704, L.909, Q.913, Q.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain C: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain C: N.1121 No protein-ligand interaction detected (PLIP)

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

NAG.12: 2 residues within 4Å: Chain A: N.318, Q.567 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: F.325, F.329, N.330 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.603, Q.631 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: H.642, N.644 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.696, G.1118 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: A.693, E.1059, N.1061 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: T.95, N.221 Chain C: K.449, E.452 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: T.95, N.221, T.223 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: N.318, P.566, Q.567 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.590 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.603, T.605 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain B: N.644 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.696, G.1118 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: N.704, Q.913, Q.1058 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: A.693, E.1059, K.1060, N.1061 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: Y.15, N.48 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain C: N.109, T.111, V.114, S.142 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: K.545 Chain C: E.268, N.269 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: N.318, Q.567 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: N.603, T.605 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: H.642, N.644 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: N.696, I.1117, G.1118 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: A.693, E.1059, N.1061 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ye, G. et al., SARS-CoV-2 spike/Nb2 complex with 1 RBD up. To Be Published

Release Date

2024-02-21

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

Spike glycoprotein

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