4HCH - 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 D-GLUCARATE DEHYDRATASE FROM AGROBACTERIUM TUMEFACIENS COMPLEXED WITH MAGNESIUM AND L-TARTRATE

Authors :   A. A. Fedorov, E. V. Fedorov, A. Sakai, J. A. Gerlt, S. C. Almo

Date :   29 Sep 12 (Deposition) - 24 Oct 12 (Release) - 24 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Enolase Fold, D-Glucarate Dehydratase, D-Glucarate, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. A. Fedorov, E. V. Fedorov, A. Sakai, J. A. Gerlt, S. C. Almo
Crystal Structure Of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed With Magnesium And L-Tartrate
To Be Published
PubMed: search

Molecule 1 - ISOMERASE/LACTONIZING ENZYME
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	ATU3453
	Organism Scientific	:	AGROBACTERIUM TUMEFACIENS
	Organism Taxid	:	176299
	Strain	:	C58 / ATCC 33970

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 20)

No.	Name	Count	Type	Full Name
1	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
2	GOL	7	Ligand/Ion	GLYCEROL
3	MG	4	Ligand/Ion	MAGNESIUM ION
4	NA	2	Ligand/Ion	SODIUM ION
5	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL
6	TLA	2	Ligand/Ion	L(+)-TARTARIC ACID

Biological Unit 1 (4, 7)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	GOL	3	Ligand/Ion	GLYCEROL
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	NA	-1	Ligand/Ion	SODIUM ION
5	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL
6	TLA	1	Ligand/Ion	L(+)-TARTARIC ACID

Biological Unit 2 (4, 56)

No.	Name	Count	Type	Full Name
1	EDO	16	Ligand/Ion	1,2-ETHANEDIOL
2	GOL	28	Ligand/Ion	GLYCEROL
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	NA	-1	Ligand/Ion	SODIUM ION
5	PGE	4	Ligand/Ion	TRIETHYLENE GLYCOL
6	TLA	8	Ligand/Ion	L(+)-TARTARIC ACID

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:24 , CYS A:139 , HIS A:171 , HIS A:209 , HIS A:309 , GOL A:402 , HOH A:527 , HOH A:555 , HOH A:585 , HOH A:708 , HOH A:950 , ARG B:90	BINDING SITE FOR RESIDUE TLA A 401
02	AC2	SOFTWARE	HIS A:309 , GLY A:310 , ASN A:311 , GLU A:329 , GLY A:331 , LEU A:332 , TLA A:401 , HOH A:586 , HOH A:733 , HOH A:951	BINDING SITE FOR RESIDUE GOL A 402
03	AC3	SOFTWARE	PRO A:181 , TYR A:211 , SER A:212 , ASP A:215 , HOH A:560 , HOH A:908	BINDING SITE FOR RESIDUE GOL A 403
04	AC4	SOFTWARE	GLU A:7 , VAL A:8 , ARG A:9 , ARG A:380 , HOH A:671 , HOH A:967	BINDING SITE FOR RESIDUE GOL A 404
05	AC5	SOFTWARE	ASP A:206 , GLU A:232 , GLU A:258 , HOH A:950 , HOH A:951 , HOH A:952	BINDING SITE FOR RESIDUE MG A 405
06	AC6	SOFTWARE	SER A:247 , LEU A:250 , HOH A:949 , HOH A:964 , HOH A:965 , HOH A:966	BINDING SITE FOR RESIDUE MG A 406
07	AC7	SOFTWARE	ASP A:206 , ALA A:207 , HIS A:209 , GLU A:232 , GLU A:233	BINDING SITE FOR RESIDUE NA A 407
08	AC8	SOFTWARE	GLN A:238 , ALA A:260 , ALA A:261 , GLY A:262 , HIS A:266 , HOH A:830 , HOH A:831 , ALA B:260 , ALA B:261 , GLY B:262 , HIS B:266 , HOH B:631	BINDING SITE FOR RESIDUE PGE A 408
09	AC9	SOFTWARE	TRP A:179	BINDING SITE FOR RESIDUE EDO A 409
10	BC1	SOFTWARE	VAL A:6 , GLU A:7 , LYS A:67 , HOH A:614 , HOH A:671 , HOH A:809 , HOH A:918 , HOH A:967	BINDING SITE FOR RESIDUE EDO A 410
11	BC2	SOFTWARE	ARG A:90 , HIS B:24 , CYS B:139 , HIS B:171 , HIS B:209 , HIS B:309 , GOL B:404 , HOH B:530 , HOH B:569 , HOH B:598 , HOH B:711 , HOH B:938	BINDING SITE FOR RESIDUE TLA B 401
12	BC3	SOFTWARE	PRO B:181 , PHE B:208 , TYR B:211 , SER B:212 , ASP B:215 , HOH B:579 , HOH B:878 , HOH B:948	BINDING SITE FOR RESIDUE GOL B 402
13	BC4	SOFTWARE	TYR B:339 , GLY B:342 , HIS B:343 , HOH B:508 , HOH B:733 , HOH B:820 , HOH B:871 , HOH B:877	BINDING SITE FOR RESIDUE GOL B 403
14	BC5	SOFTWARE	HIS B:309 , ASN B:311 , GLU B:329 , GLY B:331 , LEU B:332 , TLA B:401 , HOH B:585 , HOH B:747 , HOH B:937	BINDING SITE FOR RESIDUE GOL B 404
15	BC6	SOFTWARE	GLU B:7 , VAL B:8 , ARG B:380 , HOH B:702	BINDING SITE FOR RESIDUE GOL B 405
16	BC7	SOFTWARE	ASP B:206 , GLU B:232 , GLU B:258 , HOH B:937 , HOH B:938 , HOH B:940	BINDING SITE FOR RESIDUE MG B 406
17	BC8	SOFTWARE	SER B:247 , LEU B:250 , HOH B:936 , HOH B:939 , HOH B:941 , HOH B:942	BINDING SITE FOR RESIDUE MG B 407
18	BC9	SOFTWARE	ASP B:206 , ALA B:207 , HIS B:209 , GLU B:232 , GLU B:233	BINDING SITE FOR RESIDUE NA B 408
19	CC1	SOFTWARE	LYS B:166 , ARG B:355 , ASP B:356 , HOH B:719 , HOH B:900	BINDING SITE FOR RESIDUE EDO B 410

(no "SS Bond" information available for 4HCH)

Asymmetric Unit

No.	Residues
1	Pro A:175	-	Pro A:176
2	Ala A:180	-	Pro A:181
3	Gly A:256	-	Pro A:257
4	Gly A:331	-	Leu A:332
5	Pro B:175	-	Pro B:176
6	Ala B:180	-	Pro B:181
7	Gly B:256	-	Pro B:257
8	Gly B:331	-	Leu B:332

(no "SAP(SNP)/Variant" information available for 4HCH)

(no "PROSITE Motif" information available for 4HCH)

(no "Exon" information available for 4HCH)

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:384
                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4hcha1 A:-1-126 automated matches                                                                                              d4hcha2 A:127-382 automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeee....eeeeeehhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.hhhhhhh....eeeeeeee...........hhhhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhh....eee......hhhhhhhhhhhh...eee.....hhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhh...eee...hhhhhhhhhh......eeeeee....hhhhh...............eee...........hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hch A  -1 SHMIITDVEVRVFRTTTRRHSDSAGHAHPGPAHQVEQAMLTVRTEDGQEGHSFTAPEIVRPHVIEKFVKKVLIGEDHRDRERLWQDLAHWQRGSAAQLTDRTLAVVDCALWDLAGRSLGQPVYKLIGGYRDKVLAYGSIMCGDELEGGLATPEDYGRFAETLVKRGYKGIKLHTWMPPVSWAPDVKMDLKACAAVREAVGPDIRLMIDAFHWYSRTDALALGRGLEKLGFDWIEEPMDEQSLSSYKWLSDNLDIPVVGPESAAGKHWHRAEWIKAGACDILRTGVNDVGGITPALKTMHLAEAFGMECEVHGNTAMNLHVVAATKNCRWYERGLLHPFLEYDDGHDYLKSLSDPMDRDGFVHVPDRPGLGEDIDFTFIDNNRVR 382
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378

Chain B from PDB  Type:PROTEIN  Length:384
                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4hchb1 B:-1-126 automated matches                                                                                              d4hchb2 B:127-382 automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeee....eeeeeehhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.hhhhhhh....eeeeeeee...........hhhhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhh....eee......hhhhhhhhhhhh...eee.....hhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhh...eee...hhhhhhhhhhh.....eeeeee....hhhhh...............eee...........hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hch B  -1 SHMIITDVEVRVFRTTTRRHSDSAGHAHPGPAHQVEQAMLTVRTEDGQEGHSFTAPEIVRPHVIEKFVKKVLIGEDHRDRERLWQDLAHWQRGSAAQLTDRTLAVVDCALWDLAGRSLGQPVYKLIGGYRDKVLAYGSIMCGDELEGGLATPEDYGRFAETLVKRGYKGIKLHTWMPPVSWAPDVKMDLKACAAVREAVGPDIRLMIDAFHWYSRTDALALGRGLEKLGFDWIEEPMDEQSLSSYKWLSDNLDIPVVGPESAAGKHWHRAEWIKAGACDILRTGVNDVGGITPALKTMHLAEAFGMECEVHGNTAMNLHVVAATKNCRWYERGLLHPFLEYDDGHDYLKSLSDPMDRDGFVHVPDRPGLGEDIDFTFIDNNRVR 382
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378

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 "CATH Domain" information available for 4HCH)

(no "Pfam Domain" information available for 4HCH)

Asymmetric Unit(hide GO term definitions)

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
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PGE	[ 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 ]
		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 ]

	Cis Peptide Bonds
		Ala A:180 - Pro A:181	[ RasMol ]
		Ala B:180 - Pro B:181	[ RasMol ]
		Gly A:256 - Pro A:257	[ RasMol ]
		Gly A:331 - Leu A:332	[ RasMol ]
		Gly B:256 - Pro B:257	[ RasMol ]
		Gly B:331 - Leu B:332	[ RasMol ]
		Pro A:175 - Pro A:176	[ RasMol ]
		Pro B:175 - Pro B:176	[ 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
	4hch
		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
	Q7CSI0_AGRFC \| Q7CSI0
		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
	Q7CSI0_AGRFC \| Q7CSI0
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	Q7CSI0_AGRFC \| Q7CSI0	:	1rvk 4hcd 4hcl 4mmw

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 20)

Sites (19, 19)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

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 (0, 0)

Pfam Domains (0, 0)

Gene Ontology (4, 4)

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