3ZJ8 - 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 STRICTOSIDINE GLUCOSIDASE IN COMPLEX WITH INHIBITOR-2

Authors :   L. Xia, H. Lin, S. Panjikar, M. Ruppert, A. Castiglia, C. Rajendran, M. W H. Schuebel, H. Warzecha, V. Jaeger, J. Stoeckigt

Date :   17 Jan 13 (Deposition) - 05 Feb 14 (Release) - 22 Jul 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.01

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

Keywords :   Hydrolase, Alkaloid, Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Xia, H. Lin, A. Staniek, S. Panjikar, M. Ruppert, P. Hilgers, J. Williardt, C. Rajendran, M. Wang, H. Warzecha, V. Jager, J. Stockigt
Ligand Structures Of Synthetic Deoxa-Pyranosylamines With Raucaffricine And Strictosidine Glucosidases Provide Structural Insights Into Their Binding And Inhibitory Behaviours.
J. Enzyme. Inhib. Med. Chem. V. 30 472 2015
PubMed-ID: 25140865 | Reference-DOI: 10.3109/14756366.2014.949252

Molecule 1 - STRICTOSIDINE-O-BETA-D-GLUCOSIDASE
	Chains	:	A, B
	EC Number	:	3.2.1.105
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI M15
	Expression System Taxid	:	1007065
	Expression System Vector	:	PQE-2
	Expression System Vector Type	:	PLASMID
	Organism Common	:	SERPENTWOOD
	Organism Scientific	:	RAUVOLFIA SERPENTINA
	Organism Taxid	:	4060

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	LR1	2	Ligand/Ion	(1R,2S,3S,4R,5R)-4-[(4-BROMOPHENYL)METHYLAMINO]-5-(HYDROXYMETHYL)CYCLOPENTANE-1,2,3-TRIOL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	LR1	1	Ligand/Ion	(1R,2S,3S,4R,5R)-4-[(4-BROMOPHENYL)METHYLAMINO]-5-(HYDROXYMETHYL)CYCLOPENTANE-1,2,3-TRIOL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	LR1	1	Ligand/Ion	(1R,2S,3S,4R,5R)-4-[(4-BROMOPHENYL)METHYLAMINO]-5-(HYDROXYMETHYL)CYCLOPENTANE-1,2,3-TRIOL

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:57 , HIS A:161 , ASN A:206 , GLU A:207 , THR A:210 , ASN A:343 , TYR A:345 , TRP A:388 , GLU A:416 , TRP A:465 , GLU A:472 , TRP A:473 , TYR A:481	BINDING SITE FOR RESIDUE LR1 A1001
2	AC2	SOFTWARE	GLN B:57 , HIS B:161 , ASN B:206 , GLU B:207 , THR B:210 , TYR B:345 , TRP B:388 , GLU B:416 , TRP B:465 , GLU B:472 , TRP B:473 , TYR B:481	BINDING SITE FOR RESIDUE LR1 B1001

(no "SS Bond" information available for 3ZJ8)

Asymmetric Unit

No.	Residues
1	Ala A:222	-	Pro A:223
2	Trp A:465	-	Ser A:466
3	Ala B:222	-	Pro B:223
4	Trp B:465	-	Ser B:466

(no "SAP(SNP)/Variant" information available for 3ZJ8)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLYCOSYL_HYDROL_F1_2	PS00653	Glycosyl hydrolases family 1 N-terminal signature.	SG1_RAUSE	47-61	2	A:47-61 B:47-61

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLYCOSYL_HYDROL_F1_2	PS00653	Glycosyl hydrolases family 1 N-terminal signature.	SG1_RAUSE	47-61	1	A:47-61 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLYCOSYL_HYDROL_F1_2	PS00653	Glycosyl hydrolases family 1 N-terminal signature.	SG1_RAUSE	47-61	1	- B:47-61

(no "Exon" information available for 3ZJ8)

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:468
 aligned with SG1_RAUSE | Q8GU20 from UniProtKB/Swiss-Prot  Length:532

    Alignment length:473
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506   
            SG1_RAUSE    37 VVHRRDFPQDFIFGAGGSAYQCEGAYNEGNRGPSIWDTFTQRSPAKISDGSNGNQAINCYHMYKEDIKIMKQTGLESYRFSISWSRVLPGGRLAAGVNKDGVKFYHDFIDELLANGIKPSVTLFHWDLPQALEDEYGGFLSHRIVDDFCEYAEFCFWEFGDKIKYWTTFNEPHTFAVNGYALGEFAPGRGGKGDEGDPAIEPYVVTHNILLAHKAAVEEYRNKFQKCQEGEIGIVLNSMWMEPLSDVQADIDAQKRALDFMLGWFLEPLTTGDYPKSMRELVKGRLPKFSADDSEKLKGCYDFIGMNYYTATYVTNAVKSNSEKLSYETDDQVTKTFERNQKPIGHALYGGWQHVVPWGLYKLLVYTKETYHVPVLYVTESGMVEENKTKILLSEARRDAERTDYHQKHLASVRDAIDDGVNVKGYFVWSFFDNFEWNLGYICRYGIIHVDYKSFERYPKESAIWYKNFIAGK 509
               SCOP domains d3zj8a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh....eeeee.hhhhhh..........hhhhhhhhhhhhhh..............hhhhhhhhhhhhh..eeeee.hhhhhh...hhhhh.hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhh.....eeeeeeeeeeeee..-----..hhhhhh..............ee......eehhhhhhhhhhhhhhhhh...eeeeee...ee.....hhhhhh.hhhhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhh..ee...eee......eeehhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------GLYCOSYL_HYDROL---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zj8 A  37 VVHRRDFPQDFIFGAGGSAYQCEGAYNEGNRGPSIWDTFTQRSPAKISDGSNGNQAINCYHMYKEDIKIMKQTGLESYRFSISWSRVLPGGRLAAGVNKDGVKFYHDFIDELLANGIKPSVTLFHWDLPQALEDEYGGFLSHRIVDDFCEYAEFCFWEFGDKIKYWTTFNEPHTFAVNGYALGEFAPGRGGKGDEGDPAIEPYVVTHNILLAHKAAVEEYRNKFQKCQEGEIGIVLNSMWMEPLSDVQADIDAQKRALDFMLGWFLEPLTTGDYPKSMRELVKGRLPKFSADDSEKLKGCYDFIGMNYYTATYVTNAV-----KLSYETDDQVTKTFERNQKPIGHALYGGWQHVVPWGLYKLLVYTKETYHVPVLYVTESGMVEENKTKILLSEARRDAERTDYHQKHLASVRDAIDDGVNVKGYFVWSFFDNFEWNLGYICRYGIIHVDYKSFERYPKESAIWYKNFIAGK 509
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       | -   |   366       376       386       396       406       416       426       436       446       456       466       476       486       496       506   
                                                                                                                                                                                                                                                                                                                                                       354   360

Chain B from PDB  Type:PROTEIN  Length:467
 aligned with SG1_RAUSE | Q8GU20 from UniProtKB/Swiss-Prot  Length:532

    Alignment length:472
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507  
            SG1_RAUSE    38 VHRRDFPQDFIFGAGGSAYQCEGAYNEGNRGPSIWDTFTQRSPAKISDGSNGNQAINCYHMYKEDIKIMKQTGLESYRFSISWSRVLPGGRLAAGVNKDGVKFYHDFIDELLANGIKPSVTLFHWDLPQALEDEYGGFLSHRIVDDFCEYAEFCFWEFGDKIKYWTTFNEPHTFAVNGYALGEFAPGRGGKGDEGDPAIEPYVVTHNILLAHKAAVEEYRNKFQKCQEGEIGIVLNSMWMEPLSDVQADIDAQKRALDFMLGWFLEPLTTGDYPKSMRELVKGRLPKFSADDSEKLKGCYDFIGMNYYTATYVTNAVKSNSEKLSYETDDQVTKTFERNQKPIGHALYGGWQHVVPWGLYKLLVYTKETYHVPVLYVTESGMVEENKTKILLSEARRDAERTDYHQKHLASVRDAIDDGVNVKGYFVWSFFDNFEWNLGYICRYGIIHVDYKSFERYPKESAIWYKNFIAGK 509
               SCOP domains d3zj8b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh....eeeee.hhhhhh..........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh..eeeee.hhhhhh...hhhhh.hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhh.....eeeeeeeeeeeee..-----..hhhhhh........................hhhhhhhhhhhhhhhhh...eeeeee...ee.....hhhhhh.hhhhhhhhhhhhhhhhhhhhh...eeeeee.......hhhhh..ee...eee......eeehhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------GLYCOSYL_HYDROL---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zj8 B  38 VHRRDFPQDFIFGAGGSAYQCEGAYNEGNRGPSIWDTFTQRSPAKISDGSNGNQAINCYHMYKEDIKIMKQTGLESYRFSISWSRVLPGGRLAAGVNKDGVKFYHDFIDELLANGIKPSVTLFHWDLPQALEDEYGGFLSHRIVDDFCEYAEFCFWEFGDKIKYWTTFNEPHTFAVNGYALGEFAPGRGGKGDEGDPAIEPYVVTHNILLAHKAAVEEYRNKFQKCQEGEIGIVLNSMWMEPLSDVQADIDAQKRALDFMLGWFLEPLTTGDYPKSMRELVKGRLPKFSADDSEKLKGCYDFIGMNYYTATYVTNAV-----KLSYETDDQVTKTFERNQKPIGHALYGGWQHVVPWGLYKLLVYTKETYHVPVLYVTESGMVEENKTKILLSEARRDAERTDYHQKHLASVRDAIDDGVNVKGYFVWSFFDNFEWNLGYICRYGIIHVDYKSFERYPKESAIWYKNFIAGK 509
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347      |  -  |    367       377       387       397       407       417       427       437       447       457       467       477       487       497       507  
                                                                                                                                                                                                                                                                                                                                                      354   360

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: (Trans)glycosidases (1191)

Family: automated matches (180)

Protein domain: automated matches (180)

Rauvolfia serpentina [TaxId: 4060] (12)

1a	d3zj8a_	A:
1b	d3zj8b_	B:

(no "CATH Domain" information available for 3ZJ8)

(no "Pfam Domain" information available for 3ZJ8)

Asymmetric Unit(hide GO term definitions)

Chain A,B (SG1_RAUSE | Q8GU20)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016798	hydrolase activity, acting on glycosyl bonds	Catalysis of the hydrolysis of any glycosyl bond.
	GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	Catalysis of the hydrolysis of any O-glycosyl bond.
	GO:0050422	strictosidine beta-glucosidase activity	Catalysis of the reaction: 3alpha(S)-strictosidine + H(2)O = D-glucose + strictosidine aglycone.
biological process
	GO:0009821	alkaloid biosynthetic process	The chemical reactions and pathways resulting in the formation of alkaloids, nitrogen-containing natural products which are not otherwise classified as nonprotein amino acids, amines, peptides, amines, cyanogenic glycosides, glucosinolates, cofactors, phytohormones, or primary metabolite (such as purine or pyrimidine bases).
	GO:0009820	alkaloid metabolic process	The chemical reactions and pathways involving alkaloids, nitrogen containing natural products which are not otherwise classified as peptides, nonprotein amino acids, amines, cyanogenic glycosides, glucosinolates, cofactors, phytohormones or primary metabolites (such as purine or pyrimidine bases).
	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: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
		LR1	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
		Ala A:222 - Pro A:223	[ RasMol ]
		Ala B:222 - Pro B:223	[ RasMol ]
		Trp A:465 - Ser A:466	[ RasMol ]
		Trp B:465 - Ser B:466	[ 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
	3zj8
		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
	SG1_RAUSE \| Q8GU20
		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)
	3.2.1.105
		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
	SG1_RAUSE \| Q8GU20
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	SG1_RAUSE \| Q8GU20	:	2jf6 2jf7 3zj7

3zj6	CRYSTAL OF RAUCAFFRICINE GLUCOSIDASE IN COMPLEX WITH INHIBITOR
3zj7	CRYSTAL STRUCTURE OF STRICTOSIDINE GLUCOSIDASE IN COMPLEX WITH INHIBITOR-1

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

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