1JYM	Hydrolase	date	Sep 12, 2001
title	Crystals Of Peptide Deformylase From Plasmodium Falciparum W Subunits Per Asymmetric Unit Reveal Critical Characteristic Active Site For Drug Design
authors	A.Kumar, K.T.Nguyen, S.Srivathsan, B.Ornstein, S.Turley, I.Hirsh, W.G.J.Hol
compound		source
Molecule: Peptide Deformylase Chain: A, B, C, D, E, F, G, H, I, J Ec: 3.5.1.31 Engineered: Yes		Organism_scientific: Plasmodium Falciparum Organism_common: Malaria Parasite P. Falciparum Organism_taxid: 5833 Gene: Pdf Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet29b
symmetry	Space Group: P 41	R_factor 0.231 R_Free 0.296
crystal cell	length a length b length c angle alpha angle beta angle gamma 121.263 121.263 177.272 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.80 Å
ligand	CO, MSE	enzyme	Hydrolase E.C.3.5.1.31 BRENDA
related structures	by homologous chain: 1RQC
Primary reference	Crystals of peptide deformylase from Plasmodium falciparum reveal critical characteristics of the active site for drug design., Kumar A, Nguyen KT, Srivathsan S, Ornstein B, Turley S, Hirsh I, Pei D, Hol WG, Structure (Camb) 2002 Mar;10(3):357-67. PMID:12005434

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (299 Kb) [Save to disk] Biological Unit Coordinates (1jym.pdb1.gz) 291 Kb LPC: Ligand-Protein Contacts for 1JYM CSU: Contacts of Structural Units for 1JYM Likely Quarternary Molecular Structure file(s) for 1JYM Structure Factors (566 Kb) Retrieve 1JYM in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1JYM from S2C, [Save to disk] Re-refined 1jym structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1JYM 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 1JYM

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 1JYM, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1jyma_, region A [Jmol] [rasmolscript] [script source]     - Domain d1jymb_, region B [Jmol] [rasmolscript] [script source]     - Domain d1jymc_, region C [Jmol] [rasmolscript] [script source]     - Domain d1jymd_, region D [Jmol] [rasmolscript] [script source]     - Domain d1jyme_, region E [Jmol] [rasmolscript] [script source]     - Domain d1jymf_, region F [Jmol] [rasmolscript] [script source]     - Domain d1jymg_, region G [Jmol] [rasmolscript] [script source]     - Domain d1jymh_, region H [Jmol] [rasmolscript] [script source]     - Domain d1jymi_, region I [Jmol] [rasmolscript] [script source]     - Domain d1jymj_, region J [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: [1jym_F] [1jym_B] [1jym_J] [1jym_C] [1jym_D] [1jym_A] [1jym_E] [1jym_I] [1jym] [1jym_H] [1jym_G] SWISS-PROT database: [Q8I372] Domain organization of [Q8I372_PLAF7] by SWISSPFAM

Other resources with information on 1JYM

Community annotation for 1JYM at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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