1MKD	Hydrolase	date	Aug 29, 2002
title	Crystal Structure Of Pde4d Catalytic Domain And Zardaverine
authors	M.E.Lee, J.Markowitz, J.O.Lee, H.Lee
compound		source
Molecule: Phosphodiesterase 4d Chain: A, B, C, D, E, F, G, H, I, J, K, L Fragment: Catalytic Domain Synonym: Camp-Specific 3',5'-Cyclic Phosphodiesterase 4d Ec: 3.1.4.17 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pgex4t3
symmetry	Space Group: P 21 21 21	R_factor 0.245 R_Free 0.260
crystal cell	length a length b length c angle alpha angle beta angle gamma 97.325 164.572 325.540 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.90 Å
ligand	MG, ZAR, ZN BindingDB	enzyme	Hydrolase E.C.3.1.4.17 BRENDA
related structures	by homologous chain: 1Y2J
Gene Ontology	Chain Function Process Component F, A, J, K, E, B, H, C, D, I, G, L
Primary reference	Crystal structure of phosphodiesterase 4D and inhibitor complex(1)., Lee ME, Markowitz J, Lee JO, Lee H, FEBS Lett 2002 Oct 23;530(1-3):53-8. PMID:12387865

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (638 Kb) [Save to disk] Biological Unit Coordinates (1mkd.pdb1.gz) 320 Kb Biological Unit Coordinates (1mkd.pdb2.gz) 318 Kb LPC: Ligand-Protein Contacts for 1MKD CSU: Contacts of Structural Units for 1MKD Likely Quarternary Molecular Structure file(s) for 1MKD Retrieve 1MKD in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1MKD from S2C, [Save to disk]

View 1MKD 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 1MKD

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1MKD, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1mkda_, region A [Jmol] [rasmolscript] [script source]     - Domain d1mkdb_, region B [Jmol] [rasmolscript] [script source]     - Domain d1mkdc_, region C [Jmol] [rasmolscript] [script source]     - Domain d1mkdd_, region D [Jmol] [rasmolscript] [script source]     - Domain d1mkde_, region E [Jmol] [rasmolscript] [script source]     - Domain d1mkdf_, region F [Jmol] [rasmolscript] [script source]     - Domain d1mkdg_, region G [Jmol] [rasmolscript] [script source]     - Domain d1mkdh_, region H [Jmol] [rasmolscript] [script source]     - Domain d1mkdi_, region I [Jmol] [rasmolscript] [script source]     - Domain d1mkdj_, region J [Jmol] [rasmolscript] [script source]     - Domain d1mkdk_, region K [Jmol] [rasmolscript] [script source]     - Domain d1mkdl_, region L [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: [1mkd_D] [1mkd_A] [1mkd_B] [1mkd_H] [1mkd_L] [1mkd_J] [1mkd_K] [1mkd_G] [1mkd_F] [1mkd_E] [1mkd_I] [1mkd] [1mkd_C] SWISS-PROT database: [Q08499] Domain organization of [PDE4D_HUMAN] by SWISSPFAM Domain found in 1MKD: [HDc ] by SMART

Other resources with information on 1MKD

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

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