1D3A - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE WILD TYPE HALOPHILIC MALATE DEHYDROGENASE IN THE APO FORM

Authors :   S. B. Richard, D. Madern, E. Garcin, G. Zaccai

Date :   28 Sep 99 (Deposition) - 20 Mar 00 (Release) - 09 Apr 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.94

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (2x)

Keywords :   Rossmann Fold And 3 Sorts Of Complex Salt Bridges, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. B. Richard, D. Madern, E. Garcin, G. Zaccai
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.
Biochemistry V. 39 992 2000
PubMed-ID: 10653643 | Reference-DOI: 10.1021/BI991001A
(for further references see the PDB file header)

Molecule 1 - HALOPHILIC MALATE DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.1.1.37
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11D
	Expression System Taxid	:	562
	Organism Scientific	:	HALOARCULA MARISMORTUI
	Organism Taxid	:	2238

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	NA	1	Ligand/Ion	SODIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:205 , ASP A:306 , THR B:210B , ASP B:211	BINDING SITE FOR RESIDUE CL A 331
2	AC2	SOFTWARE	THR A:210B , ASP A:211 , LYS B:205 , ASP B:306	BINDING SITE FOR RESIDUE CL B 331
3	AC3	SOFTWARE	GLU A:247 , GLU B:247	BINDING SITE FOR RESIDUE NA A 332

(no "SS Bond" information available for 1D3A)

Asymmetric Unit

No.	Residues
1	Asn A:140	-	Pro A:141
2	Asn B:140	-	Pro B:141

(no "SAP(SNP)/Variant" information available for 1D3A)

(no "PROSITE Motif" information available for 1D3A)

(no "Exon" information available for 1D3A)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:303
 aligned with MDH_HALMA | Q07841 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:303
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301   
           MDH_HALMA      2 TKVSVVGAAGTVGAAAGYNIALRDIADEVVFVDIPDKEDDTVGQAADTNHGIAYDSNTRVRQGGYEDTAGSDVVVITAGIPRQPGQTRIDLAGDNAPIMEDIQSSLDEHNDDYISLTTSNPVDLLNRHLYEAGDRSREQVIGFGGRLDSARFRYVLSEEFDAPVQNVEGTILGEHGDAQVPVFSKVRVDGTDPEFSGDEKEQLLGDLQESAMDVIERKGATEWGPARGVAHMVEAILHDTGEVLPASVKLEGEFGHEDTAFGVPVRLGSNGVEEIVEWDLDDYEQDLMADAAEKLSDQYDKIS  304
               SCOP domains d1d3aa1 A:22-162 Malate dehydrogenase                                                                                                         d1d3aa2 A:163-330 Malate dehydrogenase                                                                                                                            SCOP domains
               CATH domains 1d3aA02 A:22-162 NAD(P)-binding Rossmann-like Domain                                                                                          1d3aA01 A:163-330 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh.....eeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhh...hhh.eee.hhhhhhhhhhhhhhhhh......ee..eee.....eee.hhhhee.......hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....eeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1d3a A   22 TKVSVVGAAGTVGAAAGYNIALRDIADEVVFVDIPDKEDDTVGQAADTNHGIAYDSNTRVRQGGYEDTAGSDVVVITAGIPRQPGQTRIDLAGDNAPIMEDIQSSLDEHNDDYISLTTSNPVDLLNRHLYEAGDRSREQVIGFGGRLDSARFRYVLSEEFDAPVQNVEGTILGEHGDAQVPVFSKVRVDGTDPEFSGDEKEQLLGDLQESAMDVIERKGATEWGPARGVAHMVEAILHDTGEVLPASVKLEGEFGHEDTAFGVPVRLGSNGVEEIVEWDLDDYEQDLMADAAEKLSDQYDKIS  330
                                   |30        40        50   |||  58        68        78  ||    90       100  ||   111       121       131||     140       150       160       170       180       190       200      210A| ||   225       235       245       255       265       275    || 286       296  ||   307       317       327   
                                 29A|                      54A||                         81|                103|                       132A|                                                                          210A| ||                                                          280|              299|                             
                                  29B                       54B|                          84                 105                        132B                                                                           210B ||                                                           282               301                             
                                                             54C                                                                                                                                                          212|                                                                                                             
                                                                                                                                                                                                                           219

Chain B from PDB  Type:PROTEIN  Length:303
 aligned with MDH_HALMA | Q07841 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:303
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301   
           MDH_HALMA      2 TKVSVVGAAGTVGAAAGYNIALRDIADEVVFVDIPDKEDDTVGQAADTNHGIAYDSNTRVRQGGYEDTAGSDVVVITAGIPRQPGQTRIDLAGDNAPIMEDIQSSLDEHNDDYISLTTSNPVDLLNRHLYEAGDRSREQVIGFGGRLDSARFRYVLSEEFDAPVQNVEGTILGEHGDAQVPVFSKVRVDGTDPEFSGDEKEQLLGDLQESAMDVIERKGATEWGPARGVAHMVEAILHDTGEVLPASVKLEGEFGHEDTAFGVPVRLGSNGVEEIVEWDLDDYEQDLMADAAEKLSDQYDKIS  304
               SCOP domains d1d3ab1 B:22-162 Malate dehydrogenase                                                                                                         d1d3ab2 B:163-330 Malate dehydrogenase                                                                                                                            SCOP domains
               CATH domains 1d3aB02 B:22-162 NAD(P)-binding Rossmann-like Domain                                                                                          1d3aB01 B:163-330 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh.....eeee..........eeee..........hhhhhhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhh...hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..eee.....eee.hhhhee.......hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....eeeee..eeehhheeee..eeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1d3a B   22 TKVSVVGAAGTVGAAAGYNIALRDIADEVVFVDIPDKEDDTVGQAADTNHGIAYDSNTRVRQGGYEDTAGSDVVVITAGIPRQPGQTRIDLAGDNAPIMEDIQSSLDEHNDDYISLTTSNPVDLLNRHLYEAGDRSREQVIGFGGRLDSARFRYVLSEEFDAPVQNVEGTILGEHGDAQVPVFSKVRVDGTDPEFSGDEKEQLLGDLQESAMDVIERKGATEWGPARGVAHMVEAILHDTGEVLPASVKLEGEFGHEDTAFGVPVRLGSNGVEEIVEWDLDDYEQDLMADAAEKLSDQYDKIS  330
                                   |30        40        50   |||  58        68        78  ||    90       100  ||   111       121       131||     140       150       160       170       180       190       200      210A| ||   225       235       245       255       265       275    || 286       296  ||   307       317       327   
                                 29A|                      54A||                         81|                103|                       132A|                                                                          210A| ||                                                          280|              299|                             
                                  29B                       54B|                          84                 105                        132B                                                                           210B ||                                                           282               301                             
                                                             54C                                                                                                                                                          212|                                                                                                             
                                                                                                                                                                                                                           219

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "Pfam Domain" information available for 1D3A)

Asymmetric Unit(hide GO term definitions)

Chain A,B (MDH_HALMA | Q07841)

molecular function
	GO:0030060	L-malate dehydrogenase activity	Catalysis of the reaction: (S)-malate + NAD+ = oxaloacetate + NADH + H+.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0019752	carboxylic acid metabolic process	The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0006099	tricarboxylic acid cycle	A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Asn A:140 - Pro A:141	[ RasMol ]
		Asn B:140 - Pro B:141	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1d3a
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	MDH_HALMA \| Q07841
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	1.1.1.37
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	MDH_HALMA \| Q07841
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	MDH_HALMA \| Q07841	:	1hlp 1o6z 2hlp 2j5k 2j5q 2j5r 2x0r 4jco

2hlp	2HLP IS THE CRYSTAL STRUCTURE OF THE E267R MUTANT OF THE HALOPHILIC MALATE DEHYDROGENASE IN THE APO FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (2, 4)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File