2PYM	Hydrolase	date	May 16, 2007
title	Hiv-1 Pr Mutant In Complex With Nelfinavir
authors	P.Rezacova, M.Kozisek, K.Saskova, J.Brynda, J.Konvalinka
compound		source
Molecule: Protease Retropepsin Chain: A, B Synonym: Hiv-1 Protease Ec: 3.4.23.16 Engineered: Yes Mutation: Yes		Organism_scientific: Human Immunodeficiency Virus 1 Organism_taxid: 11676 Strain: Type B Gene: Gag-Pol Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21 (De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet Like, T7 Promotor Driven
symmetry	Space Group: P 61	R_factor 0.193 R_Free 0.244
crystal cell	length a length b length c angle alpha angle beta angle gamma 62.218 62.218 81.415 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	1.90 Å
ligand	1UN BindingDB	enzyme	Hydrolase E.C.3.4.23.16 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	Molecular analysis of the HIV-1 resistance development: enzymatic activities, crystal structures, and thermodynamics of nelfinavir-resistant HIV protease mutants., Kozisek M, Bray J, Rezacova P, Saskova K, Brynda J, Pokorna J, Mammano F, Rulisek L, Konvalinka J, J Mol Biol. 2007 Dec 7;374(4):1005-16. Epub 2007 Oct 3. PMID:17977555

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (42 Kb) [Save to disk] Biological Unit Coordinates (2pym.pdb1.gz) 35 Kb LPC: Ligand-Protein Contacts for 2PYM CSU: Contacts of Structural Units for 2PYM Likely Quarternary Molecular Structure file(s) for 2PYM Structure Factors (201 Kb) Retrieve 2PYM in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2PYM from S2C, [Save to disk] Re-refined 2pym structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2PYM 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 2PYM

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 2PYM, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2pym_B] [2pym_A] [2pym] SWISS-PROT database: [P03367] Domain organization of [POL_HV1BR] by SWISSPFAM

Other resources with information on 2PYM

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

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