2R05	Apoptosis	date	Aug 17, 2007
title	Crystal Structure Of Alixaip1 In Complex With The Hiv-1 Yplasl Late Domain
authors	C.P.Hill, Q.Zhai, R.D.Fisher
compound		source
Molecule: Programmed Cell Death 6-Interacting Protein Chain: A Fragment: Alix Bro1-V Domains Synonym: Pdcd6-Interacting Protein, Alg-2-Interacting Protein 1, Hp95; Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Pdcd6ip, Aip1, Alix, Kiaa1375 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3) Codon+ Ril Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet151d-Topo
Molecule: P6-Gag Chain: B Fragment: Unp Residues 482-492 Engineered: Yes		Synthetic: Yes Other_details: The Sequence Of This Peptide Naturally Exists In Human Immunodeficiency Virus Type 1(Hiv-1).
symmetry	Space Group: C 1 2 1	R_factor 0.225 R_Free 0.280
crystal cell	length a length b length c angle alpha angle beta angle gamma 146.090 99.440 73.543 90.00 107.29 90.00
method	X-Ray Diffraction	resolution	2.55 Å
Primary reference	Structural and functional studies of ALIX interactions with YPX(n)L late domains of HIV-1 and EIAV., Zhai Q, Fisher RD, Chung HY, Myszka DG, Sundquist WI, Hill CP, Nat Struct Mol Biol. 2008 Jan;15(1):43-9. Epub 2007 Dec 9. PMID:18066081

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (245 Kb) [Save to disk] Biological Unit Coordinates (2r05.pdb1.gz) 238 Kb CSU: Contacts of Structural Units for 2R05 Likely Quarternary Molecular Structure file(s) for 2R05 Structure Factors (243 Kb) Retrieve 2R05 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2R05 from S2C, [Save to disk] Re-refined 2r05 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2R05 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 2R05

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 2R05, from MSDmotif at EBI Fold representative 2r05 from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2r05_A] [2r05_B] SWISS-PROT database: [P35962] [Q8WUM4] Domain organization of [GAG_HV1Y2] [PDC6I_HUMAN] by SWISSPFAM Domain found in 2R05: [BRO1 ] by SMART Alignments of the sequence of 2R05 with the sequences similar proteins can be viewed for 2R05's classification [GAG_HV1Y2] [PDC6I_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [GAG_HV1Y2] [PDC6I_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 2R05

Community annotation for 2R05 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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