SMTL ID : 5uf6.4 (4 other biounits)

The 2.8 A Electron Microscopy Structure of Adeno-Associated Virus-DJ Bound by a Heparanoid Pentasaccharide

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x ZDO- IDS- SUS- BDP- SGN: 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-methyl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside(Covalent)

ZDO-IDS-SUS-BDP-SGN.1: 4 residues within 4Å: Chain A: L.365, R.367, R.370 Chain D: R.269 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain D Water bridges: A:R.367, A:R.367, D:D.276, D:E.312 Salt bridges: A:R.367, A:R.370, D:R.269, A:R.367, A:R.367, A:R.370 ZDO-IDS-SUS-BDP-SGN.2: 3 residues within 4Å: Chain B: L.365, R.367, R.370 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.367, B:R.367 Salt bridges: B:R.367, B:R.370, B:R.367, B:R.367, B:R.370 ZDO-IDS-SUS-BDP-SGN.3: 3 residues within 4Å: Chain C: L.365, R.367, R.370 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.367, C:R.367 Salt bridges: C:R.367, C:R.370, C:R.367, C:R.367, C:R.370 ZDO-IDS-SUS-BDP-SGN.4: 4 residues within 4Å: Chain D: L.365, R.367, R.370 Chain E: R.269 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain E Water bridges: D:R.367, D:R.367, E:D.276, E:E.312 Salt bridges: D:R.367, D:R.370, E:R.269, D:R.367, D:R.367, D:R.370 ZDO-IDS-SUS-BDP-SGN.5: 4 residues within 4Å: Chain A: R.269 Chain E: L.365, R.367, R.370 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain A Water bridges: E:R.367, E:R.367, A:D.276, A:E.312 Salt bridges: E:R.367, E:R.370, A:R.269, E:R.367, E:R.367, E:R.370 ZDO-IDS-SUS-BDP-SGN.6: 3 residues within 4Å: Chain F: L.365, R.367, R.370 1 PLIP interactions: 1 interactions with chain F Water bridges: F:R.367, F:R.367 Salt bridges: F:R.367, F:R.370, F:R.367, F:R.367, F:R.370

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xie, Q. et al., The 2.8 angstrom Electron Microscopy Structure of Adeno-Associated Virus-DJ Bound by a Heparinoid Pentasaccharide. Mol Ther Methods Clin Dev (2017)

Release Date

2017-05-24

Peptides

capsid protein VP1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

capsid protein VP1

Related Entries With Identical Sequence