SMTL ID : 3j4p.4 (4 other biounits)

Electron Microscopy Analysis of a Disaccharide Analog complex Reveals Receptor Interactions of Adeno-Associated Virus

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.80 Å

Oligo State

homo-hexamer

Ligands

6 x GU4- YYJ: 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose(Post Translational Modification)

GU4-YYJ.1: 4 residues within 4Å: Chain A: R.367, R.370 Ligands: NA.2, MG.3 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.370, A:R.370, A:R.367, A:R.370 Hydrogen bonds: A:R.367 GU4-YYJ.4: 4 residues within 4Å: Chain B: R.367, R.370 Ligands: NA.5, MG.6 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.370, B:R.370, B:R.367, B:R.370 Hydrogen bonds: B:R.367 GU4-YYJ.7: 4 residues within 4Å: Chain C: R.367, R.370 Ligands: NA.8, MG.9 3 PLIP interactions: 3 interactions with chain C Salt bridges: C:R.370, C:R.370, C:R.367, C:R.370 Hydrogen bonds: C:R.367 GU4-YYJ.10: 4 residues within 4Å: Chain D: R.367, R.370 Ligands: NA.11, MG.12 3 PLIP interactions: 3 interactions with chain D Salt bridges: D:R.370, D:R.370, D:R.367, D:R.370 Hydrogen bonds: D:R.367 GU4-YYJ.13: 4 residues within 4Å: Chain E: R.367, R.370 Ligands: NA.14, MG.15 3 PLIP interactions: 3 interactions with chain E Salt bridges: E:R.370, E:R.370, E:R.367, E:R.370 Hydrogen bonds: E:R.367 GU4-YYJ.16: 4 residues within 4Å: Chain F: R.367, R.370 Ligands: NA.17, MG.18 3 PLIP interactions: 3 interactions with chain F Salt bridges: F:R.370, F:R.370, F:R.367, F:R.370 Hydrogen bonds: F:R.367

6 x NA: SODIUM ION(Non-functional Binders)

NA.2: 1 residues within 4Å: Ligands: GU4-YYJ.1 No protein-ligand interaction detected (PLIP) NA.5: 1 residues within 4Å: Ligands: GU4-YYJ.4 No protein-ligand interaction detected (PLIP) NA.8: 1 residues within 4Å: Ligands: GU4-YYJ.7 No protein-ligand interaction detected (PLIP) NA.11: 1 residues within 4Å: Ligands: GU4-YYJ.10 No protein-ligand interaction detected (PLIP) NA.14: 1 residues within 4Å: Ligands: GU4-YYJ.13 No protein-ligand interaction detected (PLIP) NA.17: 1 residues within 4Å: Ligands: GU4-YYJ.16 No protein-ligand interaction detected (PLIP)

6 x MG: MAGNESIUM ION(Non-functional Binders)

MG.3: 1 residues within 4Å: Ligands: GU4-YYJ.1 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Ligands: GU4-YYJ.4 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Ligands: GU4-YYJ.7 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Ligands: GU4-YYJ.10 No protein-ligand interaction detected (PLIP) MG.15: 1 residues within 4Å: Ligands: GU4-YYJ.13 No protein-ligand interaction detected (PLIP) MG.18: 1 residues within 4Å: Ligands: GU4-YYJ.16 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xie, Q. et al., Electron microscopy analysis of a disaccharide analog complex reveals receptor interactions of adeno-associated virus. J.Struct.Biol. (2013)

Release Date

2013-10-16

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

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