3DAP	Oxidoreductase	date	Dec 29, 1997
title	C. Glutamicum Dap Dehydrogenase In Complex With Nadp+ And Th Inhibitor 5s-Isoxazoline
authors	G.Scapin, M.Cirilli, S.G.Reddy, Y.Gao, J.C.Vederas, J.S.Blanchard
compound		source
Molecule: Diaminopimelic Acid Dehydrogenase Chain: A, B Synonym: Dapdh Ec: 1.4.1.16 Engineered: Yes		Organism_scientific: Corynebacterium Glutamicum Organism_taxid: 1718 Cell_line: Bl21 Gene: Dapdh Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21 (De3) Expression_system_plasmid: Pet23a Expression_system_gene: Dapdh
symmetry	Space Group: P 1 21 1	R_factor 0.175 R_Free 0.233
crystal cell	length a length b length c angle alpha angle beta angle gamma 75.600 65.600 84.500 90.00 106.60 90.00
method	X-Ray Diffraction	resolution	2.20 Å
ligand	DA3, NDP	enzyme	Oxidoreductase E.C.1.4.1.16 BRENDA
related structures	by homologous chain: 2DAP
Gene Ontology	Chain Function Process Component A, B
Primary reference	Substrate and inhibitor binding sites in Corynebacterium glutamicum diaminopimelate dehydrogenase., Scapin G, Cirilli M, Reddy SG, Gao Y, Vederas JC, Blanchard JS, Biochemistry 1998 Mar 10;37(10):3278-85. PMID:9521647

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (108 Kb) [Save to disk] Biological Unit Coordinates (3dap.pdb1.gz) 103 Kb LPC: Ligand-Protein Contacts for 3DAP CSU: Contacts of Structural Units for 3DAP Likely Quarternary Molecular Structure file(s) for 3DAP Structure Factors (369 Kb) Retrieve 3DAP in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3DAP from S2C, [Save to disk] Re-refined 3dap structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3DAP 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 3DAP

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 3DAP, from MSDmotif at EBI Genome occurence of 3DAP's fold from GeneCensus Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d3dapa1, region A:1-118,A:269-320 [Jmol] [rasmolscript] [script source]     - Domain d3dapa2, region A:119-268 [Jmol] [rasmolscript] [script source]     - Domain d3dapb1, region B:1-118,B:269-320 [Jmol] [rasmolscript] [script source]     - Domain d3dapb2, region B:119-268 [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: [3dap] [3dap_A] [3dap_B] SWISS-PROT database: [P04964] Domain organization of [DDH_CORGL] by SWISSPFAM

Other resources with information on 3DAP

Community annotation for 3DAP at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Domain movements in 3DAP from the Database of Macromolecular Movements. Images from IMB Jena Image Library of Biological Macromolecules.

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