SMTL ID : 7v26.1

XG005-bound SARS-CoV-2 S

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.2: 1 residues within 4Å: Chain A: N.282 Ligand excluded by PLIP NAG.3: 5 residues within 4Å: Chain A: F.338, G.339, F.342, N.343, L.368 Ligand excluded by PLIP NAG.4: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.801, Q.804 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.1098, T.1100, F.1103 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.11: 5 residues within 4Å: Chain A: C.15, V.16, N.17, C.136, N.137 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: E.132, N.165, T.167 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: G.232, N.234 Chain C: H.519 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.148, N.149, M.153 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: E.465 Chain B: N.234, T.236 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: N.280, N.282 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: F.338, G.339, N.343 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.709, G.1131 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.717, L.922, Q.1071 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.801, Q.804 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: N.1098, T.1100, F.1103 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: A.163, N.164, N.165 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: C.15, N.17, N.137 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.1074 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: H.146, N.148, N.149, M.153 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: E.132, N.164, N.165 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: H.519 Chain C: G.232, N.234 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.616, Q.644 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.709, N.710 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.1074 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain C: C.15, V.16, N.17, N.137 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.148, N.149 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain C: F.338, G.339, N.343, V.367 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Z. et al., An ultrapotent pan-beta-coronavirus lineage B ( beta-CoV-B) neutralizing antibody locks the receptor-binding domain in closed conformation by targeting its conserved epitope. Protein Cell (2022)

Release Date

2021-10-20

Peptides

Spike glycoprotein: ABC
XG005 Heavy chain: DFH
XG005 Light Chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
a

F
c

H
e

E
b

G
d

I
f

Spike glycoprotein

XG005 Heavy chain

XG005 Light Chain

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