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 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 P Protein Cleaving Enzyme, Aspartyl Protease 2, Asp 2, Asp2, 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
crystal cell	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 Diffraction	resolution	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
Gene Ontology	Chain Function Process Component A, D, C, B
Primary reference	Biochemical 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] (101 Kb) [Save to disk] Biological Unit Coordinates (1py1.pdb1.gz) 48 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

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 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] 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)

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