5A65 - 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 MOUSE THIAMINE TRIPHOSPHATASE IN COMPLEX WITH THIAMINE DIPHOSPHATE, ORTHOPHOSPHATE AND MAGNESIUM IONS.

Authors :   J. Martinez, V. Truffault, M. Hothorn

Date :   24 Jun 15 (Deposition) - 05 Aug 15 (Release) - 07 Oct 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.98

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

Keywords :   Triphosphate Tunnel Metalloenzyme, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Martinez, V. Truffault, M. Hothorn
Structural Determinants For Substrate Binding And Catalysis In Triphosphate Tunnel Metalloenzymes.
J. Biol. Chem. V. 290 23348 2015
PubMed-ID: 26221030 | Reference-DOI: 10.1074/JBC.M115.674473

Molecule 1 - THIAMINE TRIPHOSPHATASE
	Chains	:	A, B
	EC Number	:	3.6.1.28
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETM11
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	RIL
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	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 (4, 10)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	MG	4	Ligand/Ion	MAGNESIUM ION
3	PO4	2	Ligand/Ion	PHOSPHATE ION
4	TPP	2	Ligand/Ion	THIAMINE DIPHOSPHATE

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	PO4	1	Ligand/Ion	PHOSPHATE ION
4	TPP	1	Ligand/Ion	THIAMINE DIPHOSPHATE

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	PO4	1	Ligand/Ion	PHOSPHATE ION
4	TPP	1	Ligand/Ion	THIAMINE DIPHOSPHATE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:157 , GLU A:159 , MG A:501 , PO4 A:1001 , HOH A:2005 , HOH A:2006 , HOH A:2047	BINDING SITE FOR RESIDUE MG A 500
02	AC2	SOFTWARE	ASP A:145 , GLU A:159 , MG A:500 , PO4 A:1001 , HOH A:2004 , HOH A:2050	BINDING SITE FOR RESIDUE MG A 501
03	AC3	SOFTWARE	LYS A:11 , TYR A:39 , TRP A:53 , ARG A:55 , ARG A:57 , TYR A:79 , ALA A:192 , LYS A:193 , PO4 A:1001 , HOH A:2006 , HOH A:2027 , HOH A:2035 , HOH A:2036 , HOH A:2052 , HOH A:2065 , HOH A:2066 , HOH A:2067 , HOH A:2073	BINDING SITE FOR RESIDUE TPP A1000
04	AC4	SOFTWARE	ARG A:57 , ARG A:125 , ASP A:145 , GLU A:159 , MG A:500 , MG A:501 , TPP A:1000 , HOH A:2004 , HOH A:2005 , HOH A:2006 , HOH A:2039 , HOH A:2074	BINDING SITE FOR RESIDUE PO4 A1001
05	AC5	SOFTWARE	GLY A:15 , PRO A:16 , ASP A:17 , THR A:18 , GLY A:183 , VAL A:184	BINDING SITE FOR RESIDUE EDO A1100
06	AC6	SOFTWARE	GLU B:157 , GLU B:159 , PO4 B:1001 , HOH B:2001 , HOH B:2031 , HOH B:2038	BINDING SITE FOR RESIDUE MG B 500
07	AC7	SOFTWARE	ARG B:125 , ASP B:145 , GLU B:159 , PO4 B:1001 , HOH B:2002 , HOH B:2032	BINDING SITE FOR RESIDUE MG B 501
08	AC8	SOFTWARE	LYS B:11 , TYR B:39 , TRP B:53 , ARG B:55 , ARG B:57 , TYR B:79 , ALA B:192 , LYS B:193 , PO4 B:1001 , HOH B:2006 , HOH B:2017 , HOH B:2021 , HOH B:2038 , HOH B:2042 , HOH B:2043 , HOH B:2044 , HOH B:2052	BINDING SITE FOR RESIDUE TPP B1000
09	AC9	SOFTWARE	ARG B:57 , ARG B:125 , ASP B:145 , GLU B:159 , MG B:500 , MG B:501 , TPP B:1000 , HOH B:2001 , HOH B:2002 , HOH B:2023 , HOH B:2038 , HOH B:2053	BINDING SITE FOR RESIDUE PO4 B1001
10	BC1	SOFTWARE	GLY B:15 , PRO B:16 , ASP B:17 , THR B:18 , LEU B:182 , GLY B:183 , VAL B:184 , HOH B:2011	BINDING SITE FOR RESIDUE EDO B1100

(no "SS Bond" information available for 5A65)

(no "Cis Peptide Bond" information available for 5A65)

(no "SAP(SNP)/Variant" information available for 5A65)

(no "PROSITE Motif" information available for 5A65)

(no "Exon" information available for 5A65)

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:208
                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeee....hhhhhhhhh..eeeeeeeeeeeeee...hhhhhh..eeeee...eeeeeee........eeee.hhhhhhhhhhhhhh.......hhhhhhhhhh.eeeeeeeeeeeeeee......eeeeeeee...eeeeeeeeee.hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a65 A  -1 GAMTQGLIEVERKFAPGPDTEERLQELGATLEHRVTFRDTYYDTSELSLMLSDHWLRQREGSGWELKCPGVSGPHNEYVEVTSEAAIVAQLFELLGSGEQKPAGVAAVLGSLKLQEVASFITTRSSWKLALSEPQLTIDLDSADFGYAVGEVEAMVHEKAEVPAALEKIITVSSMLGVPAQEEAPAKLMVYLQRFRPLDYQRLLEAAS 214
                                     8        18        28        38        48        58        68||      81        91       101       111       121       131 ||    146       156       166       176       186       196       206        
                                                                                                 69|                                                         133|                                                                           
                                                                                                  73                                                          139

Chain B from PDB  Type:PROTEIN  Length:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeee....hhhhhhhhh..eeeeeeeeeeeeee...hhhhhh..eeeee....eeeee.....eee.hhhhhhhhhhhhh....hhhhhhhh.eeeeeeeeeeeeeeee....eeeeeeeee...eeeeeeeeee.hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a65 B  -1 GAMTQGLIEVERKFAPGPDTEERLQELGATLEHRVTFRDTYYDTSELSLMLSDHWLRQREGSGWELKCPHNEYVEVTSEAAIVAQLFELLPAGVAAVLGSLKLQEVASFITTRSSWKLALSEPQLTIDLDSADFGYAVGEVEAMVHEKAEVPAALEKIITVSSMLGVPAQEEAPAKLMVYLQRFRPLDYQRLLEAAS 214
                                     8        18        28        38        48        58        76        86        96|      112       122       132||     147       157       167       177       187       197       207       
                                                                                               67|                  96|                           133|                                                                           
                                                                                                76                  103                            139

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 5A65)

(no "CATH Domain" information available for 5A65)

(no "Pfam Domain" information available for 5A65)

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 ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		TPP	[ 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 ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5a65)

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
	5a65
		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_MOUSE \| Q8JZL3
		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_MOUSE \| Q8JZL3
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	THTPA_MOUSE \| Q8JZL3	:	2jmu 5a64

5a5y	CRYSTAL STRUCTURE OF ATTTM3 IN COMPLEX WITH TRIPOLYPHOSPHATE AND MAGNESIUM ION (FORM A)
5a60	CRYSTAL STRUCTURE OF FULL-LENGTH E. COLI YGIF IN COMPLEX WITH TRIPOLYPHOSPHATE AND TWO MAGNESIUM IONS
5a61	CRYSTAL STRUCTURE OF FULL-LENGTH E. COLI YGIF IN COMPLEX WITH TRIPOLYPHOSPHATE AND TWO MANGANESE IONS.
5a64	CRYSTAL STRUCTURE OF MOUSE THIAMINE TRIPHOSPHATASE IN COMPLEX WITH THIAMINE TRIPHOSPHATE.
5a66	CRYSTAL STRUCTURE OF ATTTM3 IN COMPLEX WITH TRIPOLYPHOSPHATE AND MANGANESE ION (FORM A)
5a67	CRYSTAL STRUCTURE OF ATTTM3 IN COMPLEX WITH TRIPOLYPHOSPHATE AND MANGANESE ION (FORM B)
5a68	CRYSTAL STRUCTURE OF THE ATTTM3 PRODUCT COMPLEX WITH TWO ORTHOPHOSPHATES AND MANGANESE IONS (FORM B)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 10)

Sites (10, 10)

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 (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