1F06	Oxidoreductase	date	May 14, 2000
title	Three Dimensional Structure Of The Ternary Complex Of Coryne Glutamicum Diaminopimelate Dehydrogenase Nadph-L-2-Amino-6- Pimelate
authors	M.Cirilli, G.Scapin, A.Sutherland, J.F.Caplan, J.C.Vederas, J.S.B
compound		source
Molecule: Meso-Diaminopimelate D-Dehydrogenase Chain: A, B Ec: 1.4.1.16 Engineered: Yes		Organism_scientific: Corynebacterium Glutamicum Organism_taxid: 1718 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet23b
symmetry	Space Group: P 1 21 1	R_factor 0.179 R_Free 0.209
crystal cell	length a length b length c angle alpha angle beta angle gamma 75.547 65.591 84.281 90.00 106.52 90.00
method	X-Ray Diffraction	resolution	2.10 Å
ligand	2NP, 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	The three-dimensional structure of the ternary complex of Corynebacterium glutamicum diaminopimelate dehydrogenase-NADPH-L-2-amino-6-methylene-pimelate., Cirilli M, Scapin G, Sutherland A, Vederas JC, Blanchard JS, Protein Sci 2000 Oct;9(10):2034-7. PMID:11106178

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (107 Kb) [Save to disk] Biological Unit Coordinates (1f06.pdb1.gz) 53 Kb Biological Unit Coordinates (1f06.pdb2.gz) 52 Kb Biological Unit Coordinates (1f06.pdb3.gz) 102 Kb LPC: Ligand-Protein Contacts for 1F06 CSU: Contacts of Structural Units for 1F06 Likely Quarternary Molecular Structure file(s) for 1F06 Structure Factors (310 Kb) Retrieve 1F06 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1F06 from S2C, [Save to disk] Re-refined 1f06 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1F06 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 1F06

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 1F06, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1f06a1, region A:1-118,A:269-320 [Jmol] [rasmolscript] [script source]     - Domain d1f06a2, region A:119-268 [Jmol] [rasmolscript] [script source]     - Domain d1f06b1, region B:501-618,B:769-820 [Jmol] [rasmolscript] [script source]     - Domain d1f06b2, region B:619-768 [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: [1f06_A] [1f06] [1f06_B] SWISS-PROT database: [P04964] Domain organization of [DDH_CORGL] by SWISSPFAM

Other resources with information on 1F06

Community annotation for 1F06 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Domain movements in 1F06 from the Database of Macromolecular Movements. Images from IMB Jena Image Library of Biological Macromolecules.

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