1D3A	Oxidoreductase	date	Sep 28, 1999
title	Crystal Structure Of The Wild Type Halophilic Malate Dehydro The Apo Form
authors	S.B.Richard, D.Madern, E.Garcin, G.Zaccai
compound		source
Molecule: Halophilic Malate Dehydrogenase Chain: A, B Ec: 1.1.1.37 Engineered: Yes		Organism_scientific: Haloarcula Marismortui Organism_taxid: 2238 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_plasmid: Pet11d
symmetry	Space Group: C 2 2 21	R_factor 0.202 R_Free 0.244
crystal cell	length a length b length c angle alpha angle beta angle gamma 115.780 131.330 125.450 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.94 Å
ligand	CL, NA	enzyme	Oxidoreductase E.C.1.1.1.37 BRENDA
related structures	by homologous chain: 1GT2
Gene Ontology	Chain Function Process Component A, B
Primary reference	Halophilic adaptation: novel solvent protein interactions observed in the 2.9 and 2.6 A resolution structures of the wild type and a mutant of malate dehydrogenase from Haloarcula marismortui., Richard SB, Madern D, Garcin E, Zaccai G, Biochemistry. 2000 Feb 8;39(5):992-1000. PMID:10653643

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (97 Kb) [Save to disk] Biological Unit Coordinates (1d3a.pdb1.gz) 183 Kb LPC: Ligand-Protein Contacts for 1D3A CSU: Contacts of Structural Units for 1D3A Likely Quarternary Molecular Structure file(s) for 1D3A Structure Factors (155 Kb) Retrieve 1D3A in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1D3A from S2C, [Save to disk] Re-refined 1d3a structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1D3A 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 1D3A

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 1D3A, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1d3aa2, region A:163-330 [Jmol] [rasmolscript] [script source]     - Domain d1d3aa1, region A:22-162 [Jmol] [rasmolscript] [script source]     - Domain d1d3ab2, region B:163-330 [Jmol] [rasmolscript] [script source]     - Domain d1d3ab1, region B:22-162 [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: [1d3a] [1d3a_A] [1d3a_B] SWISS-PROT database: [Q07841] Domain organization of [MDH_HALMA] by SWISSPFAM

Other resources with information on 1D3A

Community annotation for 1D3A at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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