1XOM	Hydrolase	date	Oct 06, 2004
title	Catalytic Domain Of Human Phosphodiesterase 4d In Complex Wi Cilomilast
authors	G.L.Card, B.P.England, Y.Suzuki, D.Fong, B.Powell, B.Lee, C.Luu, M.Tabrizizad, S.Gillette, P.N.Ibrahim, D.R.Artis, G.Bollag, M.V. S.H.Kim, J.Schlessinger, K.Y.J.Zhang
compound		source
Molecule: Camp-Specific 3',5'-Cyclic Phosphodiesterase 4d Chain: A, B Fragment: Catalytic Domain Of Human Phosphodiesterase 4d Synonym: Dpde3, Pde43 Ec: 3.1.4.17 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Pde4d Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3)Codon Plus(Ril) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet15b
symmetry	Space Group: P 21 21 21	R_factor 0.183 R_Free 0.205
crystal cell	length a length b length c angle alpha angle beta angle gamma 60.486 78.966 164.186 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.55 Å
ligand	CIO, EDO, MG, ZN BindingDB	enzyme	Hydrolase E.C.3.1.4.17 BRENDA
related structures	by homologous chain: 1TBB, 1XOR
Gene Ontology	Chain Function Process Component A, B
Primary reference	Structural basis for the activity of drugs that inhibit phosphodiesterases., Card GL, England BP, Suzuki Y, Fong D, Powell B, Lee B, Luu C, Tabrizizad M, Gillette S, Ibrahim PN, Artis DR, Bollag G, Milburn MV, Kim SH, Schlessinger J, Zhang KY, Structure (Camb) 2004 Dec;12(12):2233-47. PMID:15576036

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (128 Kb) [Save to disk] Biological Unit Coordinates (1xom.pdb1.gz) 61 Kb Biological Unit Coordinates (1xom.pdb2.gz) 62 Kb LPC: Ligand-Protein Contacts for 1XOM CSU: Contacts of Structural Units for 1XOM Likely Quarternary Molecular Structure file(s) for 1XOM Structure Factors (824 Kb) Retrieve 1XOM in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1XOM from S2C, [Save to disk] Re-refined 1xom structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1XOM 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 1XOM

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1XOM, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1xoma_, region A [Jmol] [rasmolscript] [script source]     - Domain d1xomb_, region B [Jmol] [rasmolscript] [script source]

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1xom_A] [1xom_B] [1xom] SWISS-PROT database: [Q08499] Domain organization of [PDE4D_HUMAN] by SWISSPFAM Domain found in 1XOM: [HDc ] by SMART

Other resources with information on 1XOM

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

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