3TVL - 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 :   COMPLEX BETWEEN THE HUMAN THIAMINE TRIPHOSPHATASE AND TRIPHOSPHATE

Authors :   D. Delvaux, R. Herman, E. Sauvage, P. Wins, L. Bettendorff, P. Charlier

Date :   20 Sep 11 (Deposition) - 10 Oct 12 (Release) - 17 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Hydrolase, Magnesium Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Delvaux, F. Kerff, M. R. Murty, B. Lakaye, J. Czerniecki, G. Kohn, P. Wins, R. Herman, V. Gabelica, F. Heuze, X. Tordoir, R. Maree, A. Matagne, P. Charlier, E. De Pauw, L. Bettendorff
Structural Determinants Of Specificity And Catalytic Mechanism In Mammalian 25-Kda Thiamine Triphosphatase.
Biochim. Biophys. Acta V. 1830 4513 2013
PubMed-ID: 23707715 | Reference-DOI: 10.1016/J.BBAGEN.2013.05.014

Molecule 1 - THIAMINE-TRIPHOSPHATASE
	Chains	:	A, B
	EC Number	:	3.6.1.28
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	THTPA
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	THTPASE

		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 (2, 5)

No.	Name	Count	Type	Full Name
1	3PO	2	Ligand/Ion	TRIPHOSPHATE
2	EDO	3	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	3PO	1	Ligand/Ion	TRIPHOSPHATE
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	3PO	1	Ligand/Ion	TRIPHOSPHATE
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:11 , TYR A:39 , ARG A:55 , ARG A:57 , LYS A:65 , ARG A:125 , GLU A:157 , LYS A:193 , HOH A:242 , HOH A:243 , HOH A:252 , HOH A:254 , HOH A:287	BINDING SITE FOR RESIDUE 3PO A 231
2	AC2	SOFTWARE	TYR A:39 , TYR A:40 , LEU A:47 , HIS A:52 , TRP A:53 , LEU A:54	BINDING SITE FOR RESIDUE EDO A 232
3	AC3	SOFTWARE	LYS B:11 , TYR B:39 , ARG B:55 , ARG B:57 , LYS B:65 , GLU B:81 , ARG B:125 , GLU B:157 , ALA B:192 , LYS B:193 , HOH B:238	BINDING SITE FOR RESIDUE 3PO B 231
4	AC4	SOFTWARE	PHE A:201 , ARG B:36 , THR B:38 , ARG B:56 , GLU B:58	BINDING SITE FOR RESIDUE EDO B 232
5	AC5	SOFTWARE	TYR B:39 , TYR B:40 , ASP B:41 , LEU B:47 , MET B:48 , HIS B:52 , TRP B:53 , LEU B:54 , LEU B:194	BINDING SITE FOR RESIDUE EDO B 233

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

(no "Cis Peptide Bond" information available for 3TVL)

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_062152	H	176	R	THTPA_HUMAN	Polymorphism	34015250	A/B	H	176	R

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_062152	H	176	R	THTPA_HUMAN	Polymorphism	34015250	A	H	176	R

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_062152	H	176	R	THTPA_HUMAN	Polymorphism	34015250	B	H	176	R

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTH	PS51707	CYTH domain profile.	THTPA_HUMAN	5-201	2	A:5-201 B:5-201

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTH	PS51707	CYTH domain profile.	THTPA_HUMAN	5-201	1	A:5-201 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTH	PS51707	CYTH domain profile.	THTPA_HUMAN	5-201	1	- B:5-201

(no "Exon" information available for 3TVL)

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:204
 aligned with THTPA_HUMAN | Q9BU02 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:211
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213 
          THTPA_HUMAN     4 GLIEVERKFLPGPGTEERLQELGGTLEYRVTFRDTYYDTPELSLMQADHWLRRREDSGWELKCPGAAGVLGPHTEYKELTAEPTIVAQLCKVLRADGLGAGDVAAVLGPLGLQEVASFVTKRSAWKLVLLGADEEEPQLRVDLDTADFGYAVGEVEALVHEEAEVPTALEKIHRLSSMLGVPAQETAPAKLIVYLQRFRPQDYQRLLEVNS 214
               SCOP domains d3tvla_ A: Thiamine-triphosphatase (ThTPase)                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhh..eeeeeeeeeeeeee...hhhhhh..eeeee...eeeeeee..........eeeee.hhhhhhhhhhhhhh.......hhhhhh.....eeeeeeeeeeeeeee..-------..eeeeeeee....eeeeeeeee.hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------R-------------------------------------- SAPs(SNPs)
                    PROSITE -CYTH  PDB: A:5-201 UniProt: 5-201                                                                                                                                                                    ------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tvl A   4 GLIEVERKFLPGPGTEERLQELGGTLEYRVTFRDTYYDTPELSLMQADHWLRRREDSGWELKCPGAAGVLGPHTEYKELTAEPTIVAQLCKVLRADGLGAGDVAAVLGPLGLQEVASFVTKRSAWKLVL-------PQLRVDLDTADFGYAVGEVEALVHEEAEVPTALEKIHRLSSMLGVPAQETAPAKLIVYLQRFRPQDYQRLLEVNS 214
                                    13        23        33        43        53        63        73        83        93       103       113       123        |-      |143       153       163       173       183       193       203       213 
                                                                                                                                                          132     140

Chain B from PDB  Type:PROTEIN  Length:199
 aligned with THTPA_HUMAN | Q9BU02 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:207
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       
          THTPA_HUMAN     5 LIEVERKFLPGPGTEERLQELGGTLEYRVTFRDTYYDTPELSLMQADHWLRRREDSGWELKCPGAAGVLGPHTEYKELTAEPTIVAQLCKVLRADGLGAGDVAAVLGPLGLQEVASFVTKRSAWKLVLLGADEEEPQLRVDLDTADFGYAVGEVEALVHEEAEVPTALEKIHRLSSMLGVPAQETAPAKLIVYLQRFRPQDYQRLLE 211
               SCOP domains d3tvlb_ B: Thiamine-triphosphatase (ThTPase)                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....hhhhhhhhh..eeeeeeeeeeeeee...hhhhhh..eeeee...eeeeeee..........eeeee.hhhhhhhhhhhhh........hhhhhhhhhh.eeeeeeeeeeeeeee..--------.eeeeeeee....eeeeeeeee.hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------R----------------------------------- SAPs(SNPs)
                    PROSITE CYTH  PDB: B:5-201 UniProt: 5-201                                                                                                                                                                    ---------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tvl B   5 LIEVERKFLPGPGTEERLQELGGTLEYRVTFRDTYYDTPELSLMQADHWLRRREDSGWELKCPGAAGVLGPHTEYKELTAEPTIVAQLCKVLRADGLGAGDVAAVLGPLGLQEVASFVTKRSAWKLVL--------QLRVDLDTADFGYAVGEVEALVHEEAEVPTALEKIHRLSSMLGVPAQETAPAKLIVYLQRFRPQDYQRLLE 211
                                    14        24        34        44        54        64        74        84        94       104       114       124       | -      |144       154       164       174       184       194       204       
                                                                                                                                                         132      141

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) (23004)

Fold: CYTH-like phosphatases (16)

Superfamily: CYTH-like phosphatases (16)

Family: CYTH domain (8)

Protein domain: Thiamine-triphosphatase (ThTPase) (3)

Human (Homo sapiens) [TaxId: 9606] (2)

1a	d3tvla_	A:
1b	d3tvlb_	B:

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (THTPA_HUMAN | Q9BU02)

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: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.
	GO:0050333	thiamin-triphosphatase activity	Catalysis of the reaction: H(2)O + thiamine triphosphate = H(+) + phosphate + thiamine diphosphate.
biological process
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0006091	generation of precursor metabolites and energy	The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
	GO:0042357	thiamine diphosphate metabolic process	The chemical reactions and pathways involving thiamine diphosphate, a derivative of thiamine (vitamin B1) which acts as a coenzyme in a range of processes including the Krebs cycle.
	GO:0006772	thiamine metabolic process	The chemical reactions and pathways involving thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
	GO:0042723	thiamine-containing compound metabolic process	The chemical reactions and pathways involving thiamine (vitamin B1), and compounds derived from it.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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
		3PO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		EDO	[ 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 ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3tvl)

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
	3tvl
		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
	THTPA_HUMAN \| Q9BU02
		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)
	3.6.1.28
		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
	THTPA_HUMAN \| Q9BU02
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	THTPA_HUMAN \| Q9BU02	:	3bhd

2jmu	NMR STRUCTURE OF THE MOUSE THIAMINE TRIPHOSPHATASE
3bhd	CRYSTAL STRUCTURE OF HUMAN THIAMINE TRIPHOSPHATASE (THTPA)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

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 (11, 11)

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