5IXE - 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)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   1.75A RESOLUTION STRUCTURE OF 5-FLUOROINDOLE BOUND BETA-GLYCOSIDASE (W33G) FROM SULFOLOBUS SOLFATARICUS

Authors :   S. Lovell, K. P. Battaile, N. Mehzabeen, S. J. Budiardjo, J. Karanicola

Date :   23 Mar 16 (Deposition) - 20 Jul 16 (Release) - 28 Dec 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (2x)
Biol. Unit 2: A (1x),B (1x)
Biol. Unit 3: B  (2x)
Biol. Unit 4: A,B  (2x)

Keywords :   Glycoside Hydrolase, Allosteric Activation, Switchable Enzyme, Chemical Rescue, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. J. Budiardjo, T. J. Licknack, M. B. Cory, D. Kapros, A. Roy, S. Lovell J. Douglas, J. Karanicolas
Full And Partial Agonism Of A Designed Enzyme Switch.
Acs Synth Biol V. 5 1475 2016
PubMed-ID: 27389009 | Reference-DOI: 10.1021/ACSSYNBIO.6B00097

Molecule 1 - BETA-GALACTOSIDASE
	Chains	:	A, B
	EC Number	:	3.2.1.23
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET29
	Expression System Strain	:	ROSETTA2(2DE3) PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	LACS, SSO3019
	Mutation	:	YES
	Organism Scientific	:	SULFOLOBUS SOLFATARICUS
	Organism Taxid	:	273057
	Strain	:	ATCC 35092 / DSM 1617 / JCM 11322 / P2
	Synonym	:	LACTASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	14O	2	Ligand/Ion	5-FLUORO-1H-INDOLE
2	CL	6	Ligand/Ion	CHLORIDE ION
3	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	14O	2	Ligand/Ion	5-FLUORO-1H-INDOLE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	14O	1	Ligand/Ion	5-FLUORO-1H-INDOLE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	14O	2	Ligand/Ion	5-FLUORO-1H-INDOLE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MPD	-1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 4 (2, 6)

No.	Name	Count	Type	Full Name
1	14O	4	Ligand/Ion	5-FLUORO-1H-INDOLE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:33 , VAL A:37 , TRP A:151 , PRO A:152 , GLY A:221 , PHE A:222 , PRO A:223 , TRP A:433 , ALA A:434	binding site for residue 14O A 501
2	AC2	SOFTWARE	PRO A:89 , ASN A:90 , TYR A:121 , ASN A:123 , HOH A:655 , HOH A:718 , HOH A:784 , THR B:450	binding site for residue MPD A 502
3	AC3	SOFTWARE	ASN A:264 , SER A:265 , ARG A:286 , HOH A:767	binding site for residue CL A 503
4	AC4	SOFTWARE	ARG A:440 , TYR A:448	binding site for residue CL A 504
5	AC5	SOFTWARE	ARG A:295 , HOH A:727	binding site for residue CL A 505
6	AC6	SOFTWARE	GLY B:33 , VAL B:37 , TRP B:151 , PRO B:152 , GLY B:221 , PHE B:222 , PRO B:223 , TRP B:433 , ALA B:434	binding site for residue 14O B 501
7	AC7	SOFTWARE	ASN B:264 , SER B:265 , ARG B:286 , HOH B:742	binding site for residue CL B 502
8	AC8	SOFTWARE	ARG B:295	binding site for residue CL B 503
9	AC9	SOFTWARE	ARG B:440 , TYR B:448	binding site for residue CL B 504

(no "SS Bond" information available for 5IXE)

Asymmetric Unit

No.	Residues
1	Pro A:223	-	Pro A:224
2	Trp A:425	-	Ser A:426
3	Pro B:223	-	Pro B:224
4	Trp B:425	-	Ser B:426

(no "SAP(SNP)/Variant" information available for 5IXE)

(no "PROSITE Motif" information available for 5IXE)

(no "Exon" information available for 5IXE)

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:485
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....eeeee.hhhhhh..........hhhhhhhhhhhhhhh......hhhhh.hhhhhhhhhhhhhhhh...eeeee.hhhhhh......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...........hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhee..ee..........eeeeeeeeeeeee....eee............................hhhhhhhhhhhhhhhh..eeeee.........hhhhhhhhhhhhhhhhhhh...eeeeee.......hhhhh.......eee......eeehhhhhhhhhhhhhheehhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ixe A   1 MYSFPNSFRFGWSQAGFQSEMGTPGSEDPNTDGYKWVHDPENMAAGLVSGDLPENGPGYWGNYKTFHDNAQKMGLKIARLNVEWSRIFPNPLPRPQNFDESKQDVTEVEINENELKRLDEYANKDALNHYREIFKDLKSRGLYFILNMYHWPLPLWLHDPIRVRRGDFTGPSGWLSTRTVYEFARFSAYIAWKFDDLVDEYSTMNEPNVVGGLGYVGVKSGFPPGYLSFELSRRAMYNIIQAHARAYDGIKSVSKKPVGIIYANSSFQPLTDKDMEAVEMAENDNRWWFFDAIIRGEITKIVRDDLKGRLDWIGVNYYTRTVVKRTEKGYVSLGGYGHGCERNSVSLAGLPTSDFGWEFFPEGLYDVLTKYWNRYHLYMYVTENGIADDADYQRPYYLVSHVYQVHRAINSGADVRGYLHWSLADNYEWASGFSMRFGLLKVDYNTKRLYWRPSALVYREIATNGAITDEIEHLNSVPPVKPLRH 489
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484     
                                                                                                                                                                                                                                                                                                                                    299|                                                                                                                                                                                         
                                                                                                                                                                                                                                                                                                                                     304

Chain B from PDB  Type:PROTEIN  Length:488
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....eeeee.hhhhhh..........hhhhhhhhhhhhhhh......hhhhh.hhhhhhhhhhhhhhhh...eeeee.hhhhhh......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...........hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhee.....ee..........eeeeeeeeeeeeee..eeee............................hhhhhhhhhhhhhhhh..eeeee.........hhhhhhhhhhhhhhhhhhh...eeeeee.......hhhhh.......eee......eeehhhhhhhhhhhhhheehhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ixe B   1 MYSFPNSFRFGWSQAGFQSEMGTPGSEDPNTDGYKWVHDPENMAAGLVSGDLPENGPGYWGNYKTFHDNAQKMGLKIARLNVEWSRIFPNPLPRPQNFDESKQDVTEVEINENELKRLDEYANKDALNHYREIFKDLKSRGLYFILNMYHWPLPLWLHDPIRVRRGDFTGPSGWLSTRTVYEFARFSAYIAWKFDDLVDEYSTMNEPNVVGGLGYVGVKSGFPPGYLSFELSRRAMYNIIQAHARAYDGIKSVSKKPVGIIYANSSFQPLTDKDMEAVEMAENDNRWWFFDAIIRGEITRGNKIVRDDLKGRLDWIGVNYYTRTVVKRTEKGYVSLGGYGHGCERNSVSLAGLPTSDFGWEFFPEGLYDVLTKYWNRYHLYMYVTENGIADDADYQRPYYLVSHVYQVHRAINSGADVRGYLHWSLADNYEWASGFSMRFGLLKVDYNTKRLYWRPSALVYREIATNGAITDEIEHLNSVPPVKPLRH 489
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300 ||    311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481        
                                                                                                                                                                                                                                                                                                                                       302|                                                                                                                                                                                         
                                                                                                                                                                                                                                                                                                                                        304

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 5IXE)

(no "CATH Domain" information available for 5IXE)

(no "Pfam Domain" information available for 5IXE)

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
		14O	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MPD	[ 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 ]

	Cis Peptide Bonds
		Pro A:223 - Pro A:224	[ RasMol ]
		Pro B:223 - Pro B:224	[ RasMol ]
		Trp A:425 - Ser A:426	[ RasMol ]
		Trp B:425 - Ser B:426	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ 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 \| Biol. Unit 3 PNG format \| Biol. Unit 4 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
	5ixe
		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
	BGAL_SULSO \| P22498
		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)
	3.2.1.23
		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
	BGAL_SULSO \| P22498
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	BGAL_SULSO \| P22498	:	1gow 1uwi 1uwq 1uwr 1uws 1uwt 1uwu 2ceq 2cer 4eam 4ean 5i3d

(no "Related Entries Specified in the PDB File" available for 5IXE)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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 (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