SMTL ID : 8psd.1

SARS-CoV-2 XBB 1.0 closed conformation.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: Y.25, N.27, N.58 Ligand excluded by PLIP NAG.2: 4 residues within 4Å: Chain A: T.105, N.230, T.232 Chain C: S.455 Ligand excluded by PLIP NAG.3: 4 residues within 4Å: Chain A: H.335, N.339, N.366, F.367 Ligand excluded by PLIP NAG.4: 4 residues within 4Å: Chain A: S.704, N.705 Chain B: I.790, Y.792 Ligand excluded by PLIP NAG.5: 4 residues within 4Å: Chain A: N.713, L.918, Q.922, Q.1067 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: N.797, S.799, Q.800 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.1130 Ligand excluded by PLIP NAG.8: 5 residues within 4Å: Chain A: N.612, T.614, Q.640 Chain B: I.830, Q.832 Ligand excluded by PLIP NAG.9: 5 residues within 4Å: Chain A: A.702, A.709, E.1068, N.1070 Chain B: Q.891 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: N.1094, T.1096, H.1097, F.1099 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: N.276, E.277, N.278 Chain C: K.554 Ligand excluded by PLIP NAG.12: 5 residues within 4Å: Chain A: P.326, N.327, P.575, Q.576, L.578 Ligand excluded by PLIP NAG.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain B: Y.25, N.58 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: H.335, N.339 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain B: S.704, N.705 Chain C: I.790, Y.792 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain B: T.712, N.713, L.918, Q.922, Q.1067 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: N.797, S.799, Q.800 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain B: N.1130 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain B: N.612, T.614, Q.640 Chain C: I.830, Q.832 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain B: A.702, E.1068, N.1070 Chain C: Q.891 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain B: N.1094, T.1096, H.1097, F.1099 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: K.554 Chain B: N.276, E.277, N.278 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: N.327, Q.576, L.578 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain C: Y.25, N.58 Ligand excluded by PLIP NAG.26: 8 residues within 4Å: Chain B: R.453, K.454, S.455, E.461, D.463 Chain C: T.105, N.230, T.232 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain C: N.339 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain A: Y.792 Chain C: S.704, N.705 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain C: T.712, N.713, L.918, Q.922, Q.1067 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: N.797, S.799, Q.800 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: I.1128, N.1130 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain A: I.830, Q.832 Chain C: N.612, T.614 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain C: N.1094, T.1096, H.1097, F.1099 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.276, E.277, N.278 Ligand excluded by PLIP NAG.35: 7 residues within 4Å: Chain C: P.326, N.327, I.328, P.575, Q.576, T.577, L.578 Ligand excluded by PLIP NAG.36: 6 residues within 4Å: Chain A: Q.891 Chain C: A.702, A.709, E.1068, K.1069, N.1070 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fenwick, C. et al., Broadly potent anti-SARS-CoV-2 antibody shares 93% of epitope with ACE2 and provides full protection in monkeys. J Infect (2023)

Release Date

2023-11-01

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

Spike glycoprotein