2WDD - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   TERMUS THERMOPHILUS SULFATE THIOHYDROLASE SOXB IN COMPLEX WITH SULFATE

Authors :   V. Sauve, P. Roversi, K. J. Leath, E. F. Garman, R. Antrobus, S. M. Lea, B. C. Berks

Date :   24 Mar 09 (Deposition) - 16 Jun 09 (Release) - 03 Nov 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)

Keywords :   Sulfur-Sulfur Hydrolysis, Sulfur Oxidation Pathway, Sox, Soxb, Cys S-Thiosulfonate, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Sauve, P. Roversi, K. J. Leath, E. F. Garman, R. Antrobus, S. M. Lea, B. C. Berks
Mechanism For The Hydrolysis Of A Sulfur-Sulfur Bond Based On The Crystal Structure Of The Thiosulfohydrolase Soxb.
J. Biol. Chem. V. 284 21707 2009
PubMed-ID: 19535341 | Reference-DOI: 10.1074/JBC.M109.002709

Molecule 1 - SULFUR OXIDATION PROTEIN SOXB
	Chains	:	A
	EC Number	:	3.12.2.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PVS048
	Expression System Strain	:	ROSETTA 2
	Expression System Taxid	:	562
	Expression System Variant	:	DE3
	Expression System Vector	:	PQE80L
	Fragment	:	RESIDUES 24-573
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	262724
	Other Details	:	THERMUS THERMOPHILUS HB27 SOXB
	Strain	:	HB27
	Synonym	:	SOXB

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 7)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	MN	2	Ligand/Ion	MANGANESE (II) ION
3	SO4	1	Ligand/Ion	SULFATE ION
4	TBU	3	Ligand/Ion	TERTIARY-BUTYL ALCOHOL

Biological Unit 1 (3, 5)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	SO4	1	Ligand/Ion	SULFATE ION
4	TBU	3	Ligand/Ion	TERTIARY-BUTYL ALCOHOL

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:402 , ALA A:455 , ASP A:459 , SER A:547 , HOH A:2538	BINDING SITE FOR RESIDUE ACT A1574
2	AC2	SOFTWARE	PRO A:92	BINDING SITE FOR RESIDUE TBU A1575
3	AC3	SOFTWARE	LEU A:152	BINDING SITE FOR RESIDUE TBU A1576
4	AC4	SOFTWARE	LYS A:234 , SER A:246 , PHE A:247 , ALA A:248 , HOH A:2275 , HOH A:2276	BINDING SITE FOR RESIDUE TBU A1577
5	AC5	SOFTWARE	HIS A:49 , ASP A:143 , HIS A:174 , TRP A:175 , HIS A:297 , HIS A:299 , ARG A:416 , TRP A:417 , MN A:1580 , MN A:1581 , HOH A:2414 , HOH A:2589 , HOH A:2590 , HOH A:2591	BINDING SITE FOR RESIDUE SO4 A1578
6	AC6	SOFTWARE	ASP A:47 , HIS A:49 , ASP A:143 , HIS A:299 , SO4 A:1578 , MN A:1581 , HOH A:2591	BINDING SITE FOR RESIDUE MN A1580
7	AC7	SOFTWARE	ASP A:143 , HIS A:174 , HIS A:274 , HIS A:297 , SO4 A:1578 , MN A:1580 , HOH A:2591	BINDING SITE FOR RESIDUE MN A1581

(no "SS Bond" information available for 2WDD)

(no "Cis Peptide Bond" information available for 2WDD)

(no "SAP(SNP)/Variant" information available for 2WDD)

(no "PROSITE Motif" information available for 2WDD)

(no "Exon" information available for 2WDD)

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:543
 aligned with Q72IT0_THET2 | Q72IT0 from UniProtKB/TrEMBL  Length:573

    Alignment length:543
                                    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       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570   
         Q72IT0_THET2    31 LYDLPPYGDATLLYFSDLHGQAFPHYFMEPPNLIAPKPLMGRPGYLTGEAILRYYGVERGTPLAYLLSYVDFVELARTFGPIGGMGALTALIRDQKARVEAEGGKALVLDGGDTWTNSGLSLLTRGEAVVRWQNLVGVDHMVSHWEWTLGRERVEELLGLFRGEFLSYNIVDDLFGDPLFPAYRIHRVGPYALAVVGASYPYVKVSHPESFTEGLSFALDERRLQEAVDKARAEGANAVVLLSHNGMQLDAALAERIRGIDLILSGHTHDLTPRPWRVGKTWIVAGSAAGKALMRVDLKLWKGGIANLRVRVLPVLAEHLPKAEDVEAFLKAQLAPHQDHLFTPLAVSETLLYKRDTLYSTWDQLVGEAVKAIYPEVEVVFSPAVRWGTTILPGQAITWDHLYAYTGFTYPELYLFYLRGAQIKAVLEDIASNVFTSDPFYQQGGDVSRVFGLRYVLDPDAPTGERVREVEVGGRPLDPNRRYLAAAYGGRLQRVGEAKPGYEPRPIYEVLAEYLRSVGRVRVRPEPNVKVIGRNYRLPEVTG 573
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------5_nucleotid_C-2wddA01 A:374-525                                                                                                                         ------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeeee....................hhhhh......hhhhhhhhhh....hhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..eeeeee.......hhhhhhh.hhhhhhhhhhhh..ee..hhhhhhhhhhhhhhhhhh..ee.....ee..........eeeeee..eeeeeeee...hhhhhhhhhhhh.ee...hhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhh......eeee..........eee..eeeee......eeeeeeeeee..eeeeeeeeeee..hhhh..hhhhhhhhhhhhh.hhhhhhh..eee...........hhhhhhhhhhhhhhh....eeee.............eehhhhhhhhhh....eeeeeeeehhhhhhhhhhhhhhhh.............eee.eeeee.........eeeeee..ee.....eeeeeee..hhhhhhee......eehhhhhhhhhhhhhee.......eee............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wdd A  31 LYDLPPYGDATLLYFSDLHGQAFPHYFMEPPNLIAPKPLMGRPGYLTGEAILRYYGVERGTPLAYLLSYVDFVELARTFGPIGGMGALTALIRDQKARVEAEGGKALVLDGGDTWTNSGLSLLTRGEAVVRWQNLVGVDHMVSHWEWTLGRERVEELLGLFRGEFLSYNIVDDLFGDPLFPAYRIHRVGPYALAVVGASYPYVKVSHPESFTEGLSFALDERRLQEAVDKARAEGANAVVLLSHNGMQLDAALAERIRGIDLILSGHTHDLTPRPWRVGKTWIVAGSAAGKALMRVDLKLWKGGIANLRVRVLPVLAEHLPKAEDVEAFLKAQLAPHQDHLFTPLAVSETLLYKRDTLYSTWDQLVGEAVKAIYPEVEVVFSPAVRWGTTILPGQAITWDHLYAYTGFTYPELYLFYLRGAQIKAVLEDIASNVFTSDPFYQQGGDVSRVFGLRYVLDPDAPTGERVREVEVGGRPLDPNRRYLAAAYGGRLQRVGEAKPGYEPRPIYEVLAEYLRSVGRVRVRPEPNVKVIGRNYRLPEVTG 573
                                    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       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570

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 2WDD)

(no "CATH Domain" information available for 2WDD)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: 5_nucleotid_C] (8)

Family: 5_nucleotid_C (8)

Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (3)

5_nucleotid_C-2wddA01

A:374-525

Asymmetric Unit(hide GO term definitions)

Chain A (Q72IT0_THET2 | Q72IT0)

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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0009166	nucleotide catabolic process	The chemical reactions and pathways resulting in the breakdown of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).

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
		ACT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		TBU	[ 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 ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2wdd)

Biological Unit
	Complete Structure
		Biological Unit 1	[ 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 ](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
	2wdd
		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
	Q72IT0_THET2 \| Q72IT0
		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)
	3.12.2.1
		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
	Q72IT0_THET2 \| Q72IT0
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	Q72IT0_THET2 \| Q72IT0	:	2wdc 2wde 2wdf 4uwq

2wdc	TERMUS THERMOPHILUS SULFATE THIOHYDROLASE SOXB IN COMPLEX WITH GLYCEROL
2wde	TERMUS THERMOPHILUS SULFATE THIOHYDROLASE SOXB IN COMPLEX WITH THIOSULFATE
2wdf	TERMUS THERMOPHILUS SULFATE THIOHYDROLASE SOXB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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 (1, 1)

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