3LN3 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PUTATIVE REDUCTASE (NP_038806.2) FROM MUS MUSCULUS AT 1.18 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   01 Feb 10 (Deposition) - 16 Feb 10 (Release) - 16 Feb 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.18

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

Keywords :   Putative Reductase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Reductase (Np_038806. 2) From Mus Musculus At 1. 18 A Resolution
To Be Published
PubMed: search

Molecule 1 - DIHYDRODIOL DEHYDROGENASE
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	SPEEDET
	Expression System Strain	:	HK100
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	AKR1C13, DDH
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	PUTATIVE REDUCTASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 37)

No.	Name	Count	Type	Full Name
1	MLY	28	Mod. Amino Acid	N-DIMETHYL-LYSINE
2	MRD	1	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
4	NAD	1	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
5	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (5, 37)

No.	Name	Count	Type	Full Name
1	MLY	28	Mod. Amino Acid	N-DIMETHYL-LYSINE
2	MRD	1	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
4	NAD	1	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
5	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (5, 74)

No.	Name	Count	Type	Full Name
1	MLY	56	Mod. Amino Acid	N-DIMETHYL-LYSINE
2	MRD	2	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL
3	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
4	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
5	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:171 , ARG A:175 , HOH A:360 , HOH A:453	BINDING SITE FOR RESIDUE SO4 A 324
2	AC2	SOFTWARE	GLY A:158 , MLY A:161 , HOH A:507 , HOH A:668	BINDING SITE FOR RESIDUE SO4 A 325
3	AC3	SOFTWARE	MLY A:9 , MLY A:185 , HOH A:677	BINDING SITE FOR RESIDUE SO4 A 326
4	AC4	SOFTWARE	GLY A:22 , THR A:23 , TYR A:24 , ASP A:50 , TYR A:55 , LYS A:84 , HIS A:117 , SER A:166 , ASN A:167 , GLN A:190 , TYR A:216 , GLY A:217 , ALA A:218 , LEU A:219 , GLY A:220 , THR A:221 , GLN A:222 , TYR A:224 , LEU A:236 , ALA A:253 , ALA A:269 , GLN A:270 , GLU A:276 , GLU A:279 , ASN A:280 , MRD A:328 , HOH A:353 , HOH A:390 , HOH A:567 , HOH A:625	BINDING SITE FOR RESIDUE NAD A 327
5	AC5	SOFTWARE	TYR A:55 , HIS A:117 , TYR A:118 , TRP A:227 , PHE A:310 , NAD A:327	BINDING SITE FOR RESIDUE MRD A 328

(no "SS Bond" information available for 3LN3)

(no "Cis Peptide Bond" information available for 3LN3)

(no "SAP(SNP)/Variant" information available for 3LN3)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALDOKETO_REDUCTASE_1	PS00798	Aldo/keto reductase family signature 1.	AK1CD_MOUSE	45-62	1	A:45-62
2	ALDOKETO_REDUCTASE_2	PS00062	Aldo/keto reductase family signature 2.	AK1CD_MOUSE	151-168	1	A:151-168

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALDOKETO_REDUCTASE_1	PS00798	Aldo/keto reductase family signature 1.	AK1CD_MOUSE	45-62	1	A:45-62
2	ALDOKETO_REDUCTASE_2	PS00062	Aldo/keto reductase family signature 2.	AK1CD_MOUSE	151-168	1	A:151-168

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALDOKETO_REDUCTASE_1	PS00798	Aldo/keto reductase family signature 1.	AK1CD_MOUSE	45-62	2	A:45-62
2	ALDOKETO_REDUCTASE_2	PS00062	Aldo/keto reductase family signature 2.	AK1CD_MOUSE	151-168	2	A:151-168

(no "Exon" information available for 3LN3)

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:319
 aligned with AK1CD_MOUSE | Q8VC28 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:319
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314         
          AK1CD_MOUSE     5 QHCVKLNDGHLIPALGFGTYKPKEVPKSKSLEAACLALDVGYRHVDTAYAYQVEEEIGQAIQSKIKAGVVKREDLFITTKLWCTCFRPELVKPALEKSLKKLQLDYVDLYIMHYPVPMKSGDNDFPVNEQGKSLLDTVDFCDTWERLEECKDAGLVKSIGVSNFNHRQLERILNKPGLKYKPVCNQVECHLYLNQRKLLDYCESKDIVLVAYGALGTQRYKEWVDQNSPVLLNDPVLCDVAKKNKRSPALIALRYLIQRGIVPLAQSFKENEMRENLQVFGFQLSPEDMKTLDGLNKNFRYLPAEFLVDHPEYPFVEEY 323
               SCOP domains d3ln3a_ A: automated matches                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------Aldo_ket_red-3ln3A01 A:18-301                                                                                                                                                                                                                                                               ---------------------- Pfam domains
         Sec.struct. author ..eee.....eee..eee.......hhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhhh...hhhhheeeeeehhhhhhhhhhhhhhhhhhhhhh...eeeeee..........................hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh.........eeeee......hhhhhhhhhhh..eeeee.................hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhh..hhhhhhhhhh.........hhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------ALDOKETO_REDUCTASE----------------------------------------------------------------------------------------ALDOKETO_REDUCTASE----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ln3 A   5 QHCVkLNDGHLIPALGFGTYkPkEVPkSkSLEAACLALDVGYRHVDTAYAYQVEEEIGQAIQSkIkAGVVkREDLFVTTKLWCTCFRPELVkPALEkSLkkLQLDYVDLYImHYPVPmkSGDNDFPVNEQGkSLLDTVDFCDTWERLEECkDAGLVkSIGVSNFNHRQLERILNkPGLkYkPVCNQVECHLYLNQRkLLDYCESkDIVLVAYGALGTQRYkEWVDQNSPVLLNDPVLCDVAkkNkRSPALIALRYLIQRGIVPLAQSFkENEmRENLQVFGFQLSPEDmkTLDGLNkNFRYLPAEFLVDHPEYPFVEEY 323
                                |   14        24| |   | 34        44        54        64   | |  74|       84        94 |    |104|      114 |     124       134 |     144       154|     |164       174    |  184|      194      |204    |  214       224|      234       244 || |  254       264       274  |    284       294      |304       314         
                                |              25-MLY | |                                 68-MLY  |                   96-MLY|  ||        116-MSE ||          136-MLY            155-MLY |               179-MLY |             201-MLY 209-MLY         225-MLY              246-MLY                    273-MLY             293-MSE   |                      
                                9-MLY            27-MLY |                                   70-MLY|                       101-MLY              122-MSE                                161-MLY               183-MLY                                                         247-MLY                       277-MSE          294-MLY  |                      
                                                     31-MLY                                      75-MLY                      104-MLY            123-MLY                                                       185-MLY                                                         249-MLY                                             301-MLY                  
                                                       33-MLY                                                                 105-MLY

Chain A from PDB  Type:PROTEIN  Length:319
 aligned with Q54A37_MOUSE | Q54A37 from UniProtKB/TrEMBL  Length:323

    Alignment length:319
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314         
         Q54A37_MOUSE     5 QHCVKLNDGHLIPALGFGTYKPKEVPKSKSLEAACLALDVGYRHVDTAYAYQVEEEIGQAIQSKIKAGVVKREDLFVTTKLWCTCFRPELVKPALEKSLKKLQLDYVDLYIMHYPVPMKSGDNDFPVNEQGKSLLDTVDFCDTWERLEECKDAGLVKSIGVSNFNHRQLERILNKPGLKYKPVCNQVECHLYLNQRKLLDYCESKDIVLVAYGALGTQRYKEWVDQNSPVLLNDPVLCDVAKKNKRSPALIALRYLIQRGIVPLAQSFKENEMRENLQVFGFQLSPEDMKTLDGLNKNFRYLPAEFLVDHPEYPFVEEY 323
               SCOP domains d3ln3a_ A: automated matches                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------Aldo_ket_red-3ln3A01 A:18-301                                                                                                                                                                                                                                                               ---------------------- Pfam domains
         Sec.struct. author ..eee.....eee..eee.......hhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhhh...hhhhheeeeeehhhhhhhhhhhhhhhhhhhhhh...eeeeee..........................hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh.........eeeee......hhhhhhhhhhh..eeeee.................hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhh..hhhhhhhhhh.........hhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ln3 A   5 QHCVkLNDGHLIPALGFGTYkPkEVPkSkSLEAACLALDVGYRHVDTAYAYQVEEEIGQAIQSkIkAGVVkREDLFVTTKLWCTCFRPELVkPALEkSLkkLQLDYVDLYImHYPVPmkSGDNDFPVNEQGkSLLDTVDFCDTWERLEECkDAGLVkSIGVSNFNHRQLERILNkPGLkYkPVCNQVECHLYLNQRkLLDYCESkDIVLVAYGALGTQRYkEWVDQNSPVLLNDPVLCDVAkkNkRSPALIALRYLIQRGIVPLAQSFkENEmRENLQVFGFQLSPEDmkTLDGLNkNFRYLPAEFLVDHPEYPFVEEY 323
                                |   14        24| |   | 34        44        54        64   | |  74|       84        94 |    |104|      114 |     124       134 |     144       154|     |164       174    |  184|      194      |204    |  214       224|      234       244 || |  254       264       274  |    284       294      |304       314         
                                9-MLY          25-MLY | |                                 68-MLY  |                   96-MLY|  ||        116-MSE ||          136-MLY            155-MLY |               179-MLY |             201-MLY 209-MLY         225-MLY              246-MLY                    273-MLY             293-MSE   |                      
                                                 27-MLY |                                   70-MLY|                       101-MLY              122-MSE                                161-MLY               183-MLY                                                         247-MLY                       277-MSE          294-MLY  |                      
                                                     31-MLY                                      75-MLY                      104-MLY            123-MLY                                                       185-MLY                                                         249-MLY                                             301-MLY                  
                                                       33-MLY                                                                 105-MLY

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: NAD(P)-linked oxidoreductase (286)

Family: Aldo-keto reductases (NADP) (251)

Protein domain: automated matches (62)

Mouse (Mus musculus) [TaxId: 10090] (11)

d3ln3a_

(no "CATH Domain" information available for 3LN3)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Aldo_ket_red] (94)

Family: Aldo_ket_red (94)

Mus musculus (Mouse) (2)

Aldo_ket_red-3ln3A01

A:18-301

Asymmetric Unit(hide GO term definitions)

Chain A (AK1CD_MOUSE | Q8VC28)

molecular function
	GO:0004033	aldo-keto reductase (NADP) activity	Catalysis of the reaction: an alcohol + NADP+ = an aldehyde or a ketone + NADPH + H+.
	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.
biological process
	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:0006805	xenobiotic metabolic process	The chemical reactions and pathways involving a xenobiotic compound, a compound foreign to living organisms. Used of chemical compounds, e.g. a xenobiotic chemical, such as a pesticide.

Chain A (Q54A37_MOUSE | Q54A37)

molecular function
	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.
biological process
	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.

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
		MLY	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MRD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ln3)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ 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 \| Biol. Unit 2 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
	3ln3
		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
	AK1CD_MOUSE \| Q8VC28
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	Q54A37_MOUSE \| Q54A37
		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)
	(no 'Enzyme Classificator' available)
		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
	AK1CD_MOUSE \| Q8VC28
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	Q54A37_MOUSE \| Q54A37
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	Q54A37_MOUSE \| Q54A37	:	5uxf

(no "Related Entries Specified in the PDB File" available for 3LN3)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 37)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (4, 6)

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