1PY1 Protein Transport date Jul 07, 2003
title Complex Of Gga1-Vhs Domain And Beta-Secretase C-Terminal Phosphopeptide
authors G.Zhu, X.C.Zhang
compound source
Molecule: Adp-Ribosylation Factor Binding Protein Gga1
Chain: A, B, C, D
Fragment: Vhs Domain (Residues 2-157)
Synonym: Golgi-Localized, Gamma Ear-Containing, Arf- Binding Protein 1, Gamma-Adaptin Related Protein 1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gga1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex2t

Molecule: Beta-Secretase
Chain: E, F, G, H
Fragment: C-Terminus (Residues 494-501)
Synonym: Beta-Site App Cleaving Enzyme, Beta-Site Amyloid Precursor Protein Cleaving Enzyme, Aspartyl Protease 2, Asp 2, Asp2, Membrane-Associated Aspartic Protease 2, Memapsin-2;
Ec: 3.4.23.-
Engineered: Yes

Synthetic: Yes
Other_details: Yes
symmetry Space Group: P 21 21 2
R_factor 0.236 R_Free 0.288
length a length b length c angle alpha angle beta angle gamma
70.140 95.420 107.970 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand SEP enzyme Hydrolase E.C.3.4.23 BRENDA
note 1PY1 (Molecule of the Month:pdb115)
related structures by homologous chain: 1JPL, 1UJJ
A, D, C, B

Primary referenceBiochemical and structural characterization of the interaction of memapsin 2 (beta-secretase) cytosolic domain with the VHS domain of GGA proteins., He X, Zhu G, Koelsch G, Rodgers KK, Zhang XC, Tang J, Biochemistry 2003 Oct 28;42(42):12174-80. PMID:14567678
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (102 Kb) [Save to disk]
  • Biological Unit Coordinates (1py1.pdb1.gz) 49 Kb
  • Biological Unit Coordinates (1py1.pdb2.gz) 49 Kb
  • LPC: Ligand-Protein Contacts for 1PY1
  • CSU: Contacts of Structural Units for 1PY1
  • Likely Quarternary Molecular Structure file(s) for 1PY1
  • Structure Factors (181 Kb)
  • Retrieve 1PY1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1PY1 from S2C, [Save to disk]
  • Re-refined 1py1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1PY1 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1PY1
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1PY1, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1py1a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1py1b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1py1c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1py1d_, region D [Jmol] [rasmolscript] [script source]
  • Fold representative 1py1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1py1_F] [1py1] [1py1_D] [1py1_B] [1py1_H] [1py1_E] [1py1_G] [1py1_C] [1py1_A]
  • SWISS-PROT database: [P56817] [Q9UJY5]
  • Belongs to the β-amyloid cleaving enzyme (bace1) family according to TCDB.
  • Domain organization of [BACE1_HUMAN] [GGA1_HUMAN] by SWISSPFAM
  • Domain found in 1PY1: [VHS ] by SMART
  • Other resources with information on 1PY1
  • Community annotation for 1PY1 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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