SMTL ID : 8g78.1

Local refinement of SARS-CoV-2 spike/nanobody mixture complex around NTD

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

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

NAG.1: 1 residues within 4Å: Chain A: N.221 Ligand excluded by PLIP NAG.2: 4 residues within 4Å: Chain A: N.318, S.517, Q.567 Chain F: S.7 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: N.603, Q.631 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: H.642, V.643, N.644 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.4, R.8, N.124 Ligand excluded by PLIP NAG.6: 5 residues within 4Å: Chain A: Y.15, N.48 Chain D: N.73, A.74, N.76 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: T.60, N.61 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.152 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.590 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: N.109, T.111, N.112, V.114 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.136, W.139 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.267, N.269 Chain C: K.545 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain B: N.221 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain B: N.590, T.591 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: N.603, T.605 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain B: N.644 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain B: N.4 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain B: Y.15, N.48 Chain G: N.73, A.74 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: G.59, T.60, N.61 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.152 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: E.268, N.269 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.109, A.110, N.112 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain B: N.136 Ligand excluded by PLIP NAG.24: 7 residues within 4Å: Chain C: Y.15, N.48 Chain H: F.29, N.73, A.74, K.75, N.76 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain C: N.109, T.111, N.112 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain C: N.269 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: N.318, S.517 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: N.603, T.605 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: H.642, V.643, N.644 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: N.4, L.5, N.124 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: G.59, T.60, N.61 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: E.119, N.152 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.590 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain C: H.133, N.135, N.136, S.138, W.139 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.221 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ye, G. et al., Local refinement of SARS-CoV-2 spike/nanobody mixture complex around NTD. To Be Published

Release Date

2024-02-21

Peptides

Spike glycoprotein: ABC
Nanosota-5: DGH
Nanosota-6: EFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
J

G
H

H
I

E
F

F
G

I
E

Spike glycoprotein

Nanosota-5

Nanosota-6

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