3EKG - 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)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF L-RHAMNONATE DEHYDRATASE FROM AZOTOBACTER VINELANDII COMPLEXED WITH MG AND L-TARTRATE

Authors :   A. A. Fedorov, E. V. Fedorov, J. M. Sauder, S. K. Burley, J. A. Gerlt, S. C. York Sgx Research Center For Structural Genomics (Nysgxrc)

Date :   19 Sep 08 (Deposition) - 30 Sep 08 (Release) - 09 Feb 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (4x)
Biol. Unit 2: A,B  (1x)

Keywords :   Structural Genomics, Nysgrc, L-Rhamnonate Dehydratase, Target 9265M, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. A. Fedorov, E. V. Fedorov, J. M. Sauder, S. K. Burley, J. A. Gerlt, S. C. Almo
Crystal Structure Of L-Rhamnonate Dehydratase From Azotobacter Vinelandii Complexed With Mg And L-Tartrate
To Be Published
PubMed: search

Molecule 1 - MANDELATE RACEMASE/MUCONATE LACTONIZING ENZYME
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	AVINDRAFT_6446
	Organism Scientific	:	AZOTOBACTER VINELANDII AVOP
	Organism Taxid	:	322710
	Synonym	:	L-RHAMNONATE DEHYDRATASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 34)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION
2	MSE	30	Mod. Amino Acid	SELENOMETHIONINE
3	TLA	2	Ligand/Ion	L(+)-TARTARIC ACID

Biological Unit 1 (2, 128)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	MSE	120	Mod. Amino Acid	SELENOMETHIONINE
3	TLA	8	Ligand/Ion	L(+)-TARTARIC ACID

Biological Unit 2 (2, 32)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	MSE	30	Mod. Amino Acid	SELENOMETHIONINE
3	TLA	2	Ligand/Ion	L(+)-TARTARIC ACID

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:24 , ARG A:50 , LYS A:179 , ASP A:216 , TRP A:218 , GLU A:242 , GLU A:270 , HIS A:320 , GLU A:340 , LEU A:342 , MG A:601 , HOH A:617	BINDING SITE FOR RESIDUE TLA A 501
2	AC2	SOFTWARE	ASP A:216 , GLU A:242 , GLU A:270 , TLA A:501 , HOH A:617	BINDING SITE FOR RESIDUE MG A 601
3	AC3	SOFTWARE	HIS B:24 , ARG B:50 , LYS B:179 , ASP B:216 , TRP B:218 , GLU B:242 , GLU B:270 , HIS B:320 , GLU B:340 , LEU B:342 , MG B:602 , HOH B:825 , HOH B:992	BINDING SITE FOR RESIDUE TLA B 502
4	AC4	SOFTWARE	ASP B:216 , GLU B:242 , GLU B:270 , TLA B:502 , HOH B:825	BINDING SITE FOR RESIDUE MG B 602

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

Asymmetric Unit

No.	Residues
1	His A:356	-	Pro A:357
2	His B:356	-	Pro B:357

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

(no "PROSITE Motif" information available for 3EKG)

(no "Exon" information available for 3EKG)

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:395
 aligned with C1DMY1_AZOVD | C1DMY1 from UniProtKB/TrEMBL  Length:394

    Alignment length:395
                             1                                                                                                                                                                                                                                                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389     
         C1DMY1_AZOVD     - -MSIPTIKQVRAFVLRGGGADYHDQGDGHWIDDHISTPMGKYPEYRQSRRSFGINVLGTLVVEIEASDGNVGFAVTTGGEPAAYIVEKHLARFLEGARVTDIERIWDQMYNSTLYYGRKGLVINTISGVDLALWDLLGKVRREPVHQLLGGAVRDELQFYATGARPDLAQKMGFIGGKMPLHHGPSEGEEGLKKNLEELATMRERVGPDFWLMFDCWMSLDLNYATRLARGAREYGLKWIEEALPPDDYWGYAELRRNAPTGMMVTTGEHEATRWGFRMLLEMGCCDIIQPDVGWCGGVTELLKISALADAHNALVVPHGSSVYSYHFVATRQNSPFAEFLMMAPKADQVVPMFHPQLLGEPVPENGRMRLSRLDQPGFGVTLNPECQLHRPYTH 394
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeee.............hhhhh........hhhhh..hhhhh.....eeeeeeee....eeeeeeehhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eeeeeee..hhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhh....eeee....hhhhhhhhhhhh....ee.......hhhhhhhhhhhhhhhh..ee.....hhhhhhhhh.......eeee................ee........eee.hhh.......ee............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ekg A   2 SLSIPTIKQVRAFVLRGGGADYHDQGDGHWIDDHISTPmGKYPEYRQSRRSFGINVLGTLVVEIEASDGNVGFAVTTGGEPAAYIVEKHLARFLEGARVTDIERIWDQmYNSTLYYGRKGLVINTISGVDLALWDLLGKVRREPVHQLLGGAVRDELQFYATGARPDLAQKmGFIGGKmPLHHGPSEGEEGLKKNLEELATmRERVGPDFWLmFDCWmSLDLNYATRLARGAREYGLKWIEEALPPDDYWGYAELRRNAPTGmmVTTGEHEATRWGFRmLLEmGCCDIIQPDVGWCGGVTELLKISALADAHNALVVPHGSSVYSYHFVATRQNSPFAEFLmmAPKADQVVPmFHPQLLGEPVPENGRmRLSRLDQPGFGVTLNPECQLHRPYTH 396
                                    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       311       321       331       341 ||    351  |    361       371       381       391     
                                                                 40-MSE                                                               110-MSE                                                        173-MSE  |                    203-MSE    214-MSE|                                          264-MSE         280-MSE                                                        343-MSE    354-MSE         370-MSE                      
                                                                                                                                                                                                            180-MSE                                219-MSE                                       265-MSE            284-MSE                                                     344-MSE

Chain B from PDB  Type:PROTEIN  Length:395
 aligned with C1DMY1_AZOVD | C1DMY1 from UniProtKB/TrEMBL  Length:394

    Alignment length:395
                             1                                                                                                                                                                                                                                                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389     
         C1DMY1_AZOVD     - -MSIPTIKQVRAFVLRGGGADYHDQGDGHWIDDHISTPMGKYPEYRQSRRSFGINVLGTLVVEIEASDGNVGFAVTTGGEPAAYIVEKHLARFLEGARVTDIERIWDQMYNSTLYYGRKGLVINTISGVDLALWDLLGKVRREPVHQLLGGAVRDELQFYATGARPDLAQKMGFIGGKMPLHHGPSEGEEGLKKNLEELATMRERVGPDFWLMFDCWMSLDLNYATRLARGAREYGLKWIEEALPPDDYWGYAELRRNAPTGMMVTTGEHEATRWGFRMLLEMGCCDIIQPDVGWCGGVTELLKISALADAHNALVVPHGSSVYSYHFVATRQNSPFAEFLMMAPKADQVVPMFHPQLLGEPVPENGRMRLSRLDQPGFGVTLNPECQLHRPYTH 394
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeee.............hhhhh........hhhhh.hhhhhh.....eeeeeeee....eeeeeeehhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eeeeeee..hhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhh....eeee....hhhhhhhhhhhh....ee.......hhhhhhhhhhhhhhhh..ee.....hhhhhhhhh.......eeee................ee........eee.hhh.......ee............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ekg B   2 SLSIPTIKQVRAFVLRGGGADYHDQGDGHWIDDHISTPmGKYPEYRQSRRSFGINVLGTLVVEIEASDGNVGFAVTTGGEPAAYIVEKHLARFLEGARVTDIERIWDQmYNSTLYYGRKGLVINTISGVDLALWDLLGKVRREPVHQLLGGAVRDELQFYATGARPDLAQKmGFIGGKmPLHHGPSEGEEGLKKNLEELATmRERVGPDFWLmFDCWmSLDLNYATRLARGAREYGLKWIEEALPPDDYWGYAELRRNAPTGmmVTTGEHEATRWGFRmLLEmGCCDIIQPDVGWCGGVTELLKISALADAHNALVVPHGSSVYSYHFVATRQNSPFAEFLmmAPKADQVVPmFHPQLLGEPVPENGRmRLSRLDQPGFGVTLNPECQLHRPYTH 396
                                    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       311       321       331       341 ||    351  |    361       371       381       391     
                                                                 40-MSE                                                               110-MSE                                                        173-MSE  |                    203-MSE    214-MSE|                                          264-MSE         280-MSE                                                        343-MSE    354-MSE         370-MSE                      
                                                                                                                                                                                                            180-MSE                                219-MSE                                       265-MSE            284-MSE                                                     344-MSE

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 "SCOP Domain" information available for 3EKG)

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

(no "Pfam Domain" information available for 3EKG)

Asymmetric Unit(hide GO term definitions)

Chain A,B (C1DMY1_AZOVD | C1DMY1)

molecular function
	GO:0050032	L-rhamnonate dehydratase activity	Catalysis of the reaction: L-rhamnonate = 2-dehydro-3-deoxy-L-rhamnonate + H(2)O.
	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: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.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0009063	cellular amino acid catabolic process	The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		TLA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
		His A:356 - Pro A:357	[ RasMol ]
		His B:356 - Pro B:357	[ RasMol ]

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
	3ekg
		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
	C1DMY1_AZOVD \| C1DMY1
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

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
	C1DMY1_AZOVD \| C1DMY1
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	C1DMY1_AZOVD \| C1DMY1	:	2oz3

2oz3	THE SAME PROTEIN WITHOUT MG AND L-TARTRATE BOUND, CRYSTALLIZED IN DIFFERENT SPACE GROUP RELATED ID: NYSGXRC-9265M RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 34)

Sites (4, 4)

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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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