3KER - 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 :   D-DOPACHROME TAUTOMERASE (D-DT)/ MACROPHAGE MIGRATION INHIBITORY FACTOR 2 (MIF2) COMPLEXED WITH INHIBITOR 4-IPP

Authors :   S. Zierow, E. Lolis

Date :   26 Oct 09 (Deposition) - 13 Oct 10 (Release) - 06 Apr 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.78

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

Keywords :   Tautomerase, Inflammation, Cytokine, Cytokine-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Zierow, E. Lolis
Solution Structure Of D-Dt/Mif2 Complexed With 4-Ipp
To Be Published
PubMed: search

Molecule 1 - D-DOPACHROME DECARBOXYLASE
	Chains	:	A, B, C, D
	EC Number	:	4.1.1.84
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DDT
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	D-DOPACHROME TAUTOMERASE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B	C
Biological Unit 2 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 20)

No.	Name	Count	Type	Full Name
1	CL	12	Ligand/Ion	CHLORIDE ION
2	NA	4	Ligand/Ion	SODIUM ION
3	RW1	4	Ligand/Ion	4-PHENYLPYRIMIDINE

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	NA	-1	Ligand/Ion	SODIUM ION
3	RW1	3	Ligand/Ion	4-PHENYLPYRIMIDINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	NA	-1	Ligand/Ion	SODIUM ION
3	RW1	1	Ligand/Ion	4-PHENYLPYRIMIDINE

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PRO A:1 , PHE A:2 , PRO A:33 , ARG A:36 , ILE A:107 , LYS A:109 , MET A:114 , CL A:118 , LEU D:117	BINDING SITE FOR RESIDUE RW1 A 120
02	AC2	SOFTWARE	PRO A:1 , LYS A:32 , SER A:63 , ILE A:64 , RW1 A:120	BINDING SITE FOR RESIDUE CL A 118
03	AC3	SOFTWARE	PRO A:10 , ALA A:11	BINDING SITE FOR RESIDUE CL A 119
04	AC4	SOFTWARE	THR A:46	BINDING SITE FOR RESIDUE NA A 121
05	AC5	SOFTWARE	ASN A:8 , THR A:46 , LEU A:47	BINDING SITE FOR RESIDUE CL A 122
06	AC6	SOFTWARE	PRO B:1 , PHE B:2 , PRO B:33 , ARG B:36 , ILE B:107 , LYS B:109 , MET B:114 , CL B:118	BINDING SITE FOR RESIDUE RW1 B 120
07	AC7	SOFTWARE	PRO B:1 , LYS B:32 , SER B:63 , ILE B:64 , RW1 B:120	BINDING SITE FOR RESIDUE CL B 118
08	AC8	SOFTWARE	PRO B:10 , ALA B:11	BINDING SITE FOR RESIDUE CL B 119
09	AC9	SOFTWARE	PRO A:43 , THR B:46	BINDING SITE FOR RESIDUE NA B 121
10	BC1	SOFTWARE	ASN B:8 , THR B:46 , LEU B:47	BINDING SITE FOR RESIDUE CL B 122
11	BC2	SOFTWARE	LEU B:117 , PRO C:1 , PHE C:2 , PRO C:33 , ARG C:36 , ILE C:107 , LYS C:109 , MET C:114 , CL C:118	BINDING SITE FOR RESIDUE RW1 C 120
12	BC3	SOFTWARE	PRO C:1 , LYS C:32 , SER C:63 , ILE C:64 , RW1 C:120	BINDING SITE FOR RESIDUE CL C 118
13	BC4	SOFTWARE	PRO C:10 , ALA C:11	BINDING SITE FOR RESIDUE CL C 119
14	BC5	SOFTWARE	THR C:46	BINDING SITE FOR RESIDUE NA C 121
15	BC6	SOFTWARE	ASN C:8 , THR C:46 , LEU C:47	BINDING SITE FOR RESIDUE CL C 122
16	BC7	SOFTWARE	PRO D:1 , PHE D:2 , PRO D:33 , ARG D:36 , ILE D:107 , LYS D:109 , MET D:114 , CL D:118	BINDING SITE FOR RESIDUE RW1 D 120
17	BC8	SOFTWARE	PRO D:1 , LYS D:32 , SER D:63 , ILE D:64 , RW1 D:120	BINDING SITE FOR RESIDUE CL D 118
18	BC9	SOFTWARE	PRO D:10 , ALA D:11	BINDING SITE FOR RESIDUE CL D 119
19	CC1	SOFTWARE	THR D:46	BINDING SITE FOR RESIDUE NA D 121
20	CC2	SOFTWARE	ASN D:8 , THR D:46 , LEU D:47	BINDING SITE FOR RESIDUE CL D 122

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

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

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MIF	PS01158	Macrophage migration inhibitory factor family signature.	DOPD_MOUSE	55-69	4	A:54-68 B:54-68 C:54-68 D:54-68

Biological Unit 1 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MIF	PS01158	Macrophage migration inhibitory factor family signature.	DOPD_MOUSE	55-69	3	A:54-68 B:54-68 C:54-68 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MIF	PS01158	Macrophage migration inhibitory factor family signature.	DOPD_MOUSE	55-69	1	- - - D:54-68

(no "Exon" information available for 3KER)

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:117
 aligned with DOPD_MOUSE | O35215 from UniProtKB/Swiss-Prot  Length:118

    Alignment length:117
                                    11        21        31        41        51        61        71        81        91       101       111       
           DOPD_MOUSE     2 PFVELETNLPASRIPAGLENRLCAATATILDKPEDRVSVTIRPGMTLLMNKSTEPCAHLLVSSIGVVGTAEQNRTHSASFFKFLTEELSLDQDRIVIRFFPLEAWQIGKKGTVMTFL 118
               SCOP domains d3kera_ A: automated matches                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhh..hhhhhhhhhhhhhhh.hhhh.eeeee...eee........eeeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeeehhh.eee..ee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------MIF            ------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3ker A   1 PFVELETNLPASRIPAGLENRLCAATATILDKPEDRVSVTIRPGMTLLMNKSTEPCAHLLVSSIGVVGTAEQNRTHSASFFKFLTEELSLDQDRIVIRFFPLEAWQIGKKGTVMTFL 117
                                    10        20        30        40        50        60        70        80        90       100       110

Chain B from PDB  Type:PROTEIN  Length:117
 aligned with DOPD_MOUSE | O35215 from UniProtKB/Swiss-Prot  Length:118

    Alignment length:117
                                    11        21        31        41        51        61        71        81        91       101       111       
           DOPD_MOUSE     2 PFVELETNLPASRIPAGLENRLCAATATILDKPEDRVSVTIRPGMTLLMNKSTEPCAHLLVSSIGVVGTAEQNRTHSASFFKFLTEELSLDQDRIVIRFFPLEAWQIGKKGTVMTFL 118
               SCOP domains d3kerb_ B: automated matches                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhh..hhhhhhhhhhhhhhh.hhhh.eeeee...eeee.......eeeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeeehhh.eee..ee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------MIF            ------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3ker B   1 PFVELETNLPASRIPAGLENRLCAATATILDKPEDRVSVTIRPGMTLLMNKSTEPCAHLLVSSIGVVGTAEQNRTHSASFFKFLTEELSLDQDRIVIRFFPLEAWQIGKKGTVMTFL 117
                                    10        20        30        40        50        60        70        80        90       100       110

Chain C from PDB  Type:PROTEIN  Length:117
 aligned with DOPD_MOUSE | O35215 from UniProtKB/Swiss-Prot  Length:118

    Alignment length:117
                                    11        21        31        41        51        61        71        81        91       101       111       
           DOPD_MOUSE     2 PFVELETNLPASRIPAGLENRLCAATATILDKPEDRVSVTIRPGMTLLMNKSTEPCAHLLVSSIGVVGTAEQNRTHSASFFKFLTEELSLDQDRIVIRFFPLEAWQIGKKGTVMTFL 118
               SCOP domains d3kerc_ C: automated matches                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhh..hhhhhhhhhhhhhhh.hhhhheeeee...eeee.......eeeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeeehhh.eee..ee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------MIF            ------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3ker C   1 PFVELETNLPASRIPAGLENRLCAATATILDKPEDRVSVTIRPGMTLLMNKSTEPCAHLLVSSIGVVGTAEQNRTHSASFFKFLTEELSLDQDRIVIRFFPLEAWQIGKKGTVMTFL 117
                                    10        20        30        40        50        60        70        80        90       100       110

Chain D from PDB  Type:PROTEIN  Length:117
 aligned with DOPD_MOUSE | O35215 from UniProtKB/Swiss-Prot  Length:118

    Alignment length:117
                                    11        21        31        41        51        61        71        81        91       101       111       
           DOPD_MOUSE     2 PFVELETNLPASRIPAGLENRLCAATATILDKPEDRVSVTIRPGMTLLMNKSTEPCAHLLVSSIGVVGTAEQNRTHSASFFKFLTEELSLDQDRIVIRFFPLEAWQIGKKGTVMTFL 118
               SCOP domains d3kerd_ D: automated matches                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) MIF-3kerD01 D:1-115                                                                                                -- Pfam domains (1)
           Pfam domains (2) MIF-3kerD02 D:1-115                                                                                                -- Pfam domains (2)
           Pfam domains (3) MIF-3kerD03 D:1-115                                                                                                -- Pfam domains (3)
           Pfam domains (4) MIF-3kerD04 D:1-115                                                                                                -- Pfam domains (4)
         Sec.struct. author .eeeeee..hhhhh..hhhhhhhhhhhhhhh.hhhhheeeee..............eeeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeeehhhh.ee..ee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------MIF            ------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3ker D   1 PFVELETNLPASRIPAGLENRLCAATATILDKPEDRVSVTIRPGMTLLMNKSTEPCAHLLVSSIGVVGTAEQNRTHSASFFKFLTEELSLDQDRIVIRFFPLEAWQIGKKGTVMTFL 117
                                    10        20        30        40        50        60        70        80        90       100       110

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) (23004)

Fold: Tautomerase/MIF (104)

Superfamily: Tautomerase/MIF (104)

Family: MIF-related (58)

Protein domain: automated matches (1)

Mouse (Mus musculus) [TaxId: 10090] (1)

1a	d3kera_	A:
1b	d3kerb_	B:
1c	d3kerc_	C:
1d	d3kerd_	D:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: MIF (36)

Family: MIF (22)

Mus musculus (Mouse) (3)

1a	MIF-3kerD01	D:1-115
1b	MIF-3kerD02	D:1-115
1c	MIF-3kerD03	D:1-115
1d	MIF-3kerD04	D:1-115

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (DOPD_MOUSE | O35215)

molecular function
	GO:0033981	D-dopachrome decarboxylase activity	Catalysis of the reaction: D-dopachrome + H(+) = 5,6-dihydroxyindole + CO(2).
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
	GO:0042438	melanin biosynthetic process	The chemical reactions and pathways resulting in the formation of melanins, pigments largely of animal origin. High molecular weight polymers of indole quinone, they are irregular polymeric structures and are divided into three groups: allomelanins in the plant kingdom and eumelanins and phaeomelanins in the animal kingdom.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

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 ]
		RW1	[ 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 ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]
		BC9	[ RasMol ]	+environment [ RasMol ]
		CC1	[ RasMol ]	+environment [ RasMol ]
		CC2	[ RasMol ]	+environment [ RasMol ]

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

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
	3ker
		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
	DOPD_MOUSE \| O35215
		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)
	4.1.1.84
		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
	DOPD_MOUSE \| O35215
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 3KER)

1dpt	D-DOPACHROME TAUTOMERASE
1mif	MACROPHAGE MIGRATION INHIBITORY FACTOR (MIF)
3b64	MACROPHAGE MIGRATION INHIBITORY FACTOR (MIF) FROM LEISHMANIA MAJOR
3b9s	MACROPHAGE MIGRATION INHIBITORY FACTOR (MIF) COMPLEXED WITH INHIBITOR, 4-IPP
3kan	D-DOPACHROME TAUTOMERASE (D-DT)/MACROPHAGE MIGRATION INHIBITORY FACTOR 2 (MIF2) COMPLEXED WITH INHIBITOR 4-IPP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 20)

Sites (20, 20)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (1, 4)

Gene Ontology (5, 5)

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