2F7K - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN PYRIDOXAL KINASE

Authors :   T. Jiang, P. Cao, Y. Gong, L. Tang

Date :   01 Dec 05 (Deposition) - 13 Jun 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym./Biol. Unit : A,B

Keywords :   Alpha-Beta Structure, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Cao, Y. Gong, L. Tang, Y. C. Leung, T. Jiang
Crystal Structure Of Human Pyridoxal Kinase
J. Struct. Biol. V. 154 327 2006
PubMed-ID: 16600635 | Reference-DOI: 10.1016/J.JSB.2006.02.008
(for further references see the PDB file header)

Molecule 1 - PYRIDOXAL KINASE
	Chains	:	A, B
	EC Number	:	2.7.1.35
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRECEIVER-B01A
	Expression System Strain	:	BL21 (DE3) PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PYRIDOXINE KINASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2F7K)

(no "Site" information available for 2F7K)

(no "SS Bond" information available for 2F7K)

(no "Cis Peptide Bond" information available for 2F7K)

(no "SAP(SNP)/Variant" information available for 2F7K)

(no "PROSITE Motif" information available for 2F7K)

Asymmetric/Biological Unit (11, 22)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1c	ENST00000291565	1c	ENSE00001861574	chr21:45138993-45139262	270	PDXK_HUMAN	1-29	29	2	A:1-29 B:1-29	29 29
1.6	ENST00000291565	6	ENSE00001050589	chr21:45153950-45154004	55	PDXK_HUMAN	30-48	19	2	A:30-48 B:30-48	19 19
1.9e	ENST00000291565	9e	ENSE00001050594	chr21:45161548-45161652	105	PDXK_HUMAN	48-83	36	2	A:48-83 B:48-83	36 36
1.10b	ENST00000291565	10b	ENSE00001050590	chr21:45163605-45163688	84	PDXK_HUMAN	83-111	29	2	A:83-111 B:83-111	29 29
1.12b	ENST00000291565	12b	ENSE00001050584	chr21:45165960-45166006	47	PDXK_HUMAN	111-126	16	2	A:111-126 B:111-126	16 16
1.14	ENST00000291565	14	ENSE00001050578	chr21:45168876-45168961	86	PDXK_HUMAN	127-155	29	2	A:127-155 B:127-155	29 29
1.15	ENST00000291565	15	ENSE00001050582	chr21:45170381-45170426	46	PDXK_HUMAN	155-170	16	2	A:155-170 B:155-170	16 16
1.16	ENST00000291565	16	ENSE00001050593	chr21:45172399-45172510	112	PDXK_HUMAN	171-208	38	2	A:171-208 B:171-208	38 38
1.17c	ENST00000291565	17c	ENSE00001050587	chr21:45173464-45173600	137	PDXK_HUMAN	208-253	46	2	A:208-253 B:208-253	46 46
1.18b	ENST00000291565	18b	ENSE00001050583	chr21:45175579-45175645	67	PDXK_HUMAN	254-276	23	2	A:254-276 B:254-276	23 23
1.19e	ENST00000291565	19e	ENSE00001431057	chr21:45175832-45182188	6357	PDXK_HUMAN	276-312	37	2	A:276-312 B:276-312	37 37

Asymmetric/Biological 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:323
 aligned with PDXK_HUMAN | O00764 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:323
                                       1                                                                                                                                                                                                                                                                                                                       
                                     - |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309   
           PDXK_HUMAN     - -----------MEEECRVLSIQSHVIRGYVGNRAATFPLQVLGFEIDAVNSVQFSNHTGYAHWKGQVLNSDELQELYEGLRLNNMNKYDYVLTGYTRDKSFLAMVVDIVQELKQQNPRLVYVCDPVLGDKWDGEGSMYVPEDLLPVYKEKVVPLADIITPNQFEAELLSGRKIHSQEEALRVMDMLHSMGPDTVVITSSDLPSPQGSNYLIVLGSQRRRNPAGSVVMERIRMDIRKVDAVFVGTGDLFAAMLLAWTHKHPNNLKVACEKTVSTLHHVLQRTIQCAKAQAGEGVRPSPMQLELRMVQSKRDIEDPEIVVQATVL 312
               SCOP domains d2f7ka_ A: automated matches                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2f7kA00 A:-10-312  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeeeeeee.....hhhhhhhhhhhh.eeeeeeeeeee..........eee.hhhhhhhhhhhhhhh.......eee....hhhhhhhhhhhhhhhhhhh....eee....eee....eee....hhhhhhhhhhhhhh.ee..hhhhhhhhhh....hhhhhhhhhhhhhhh...eeee............eeeeeeeeeeee...eeeeeeeeeeee.......hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhh.......eee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) -----------Exon 1.1c  PDB: A:1-29       Exon 1.6           ----------------------------------Exon 1.10b  PDB: A:83-111    ---------------Exon 1.14  PDB: A:127-155    ---------------Exon 1.16  PDB: A:171-208             ---------------------------------------------Exon 1.18b             ------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------Exon 1.9e  PDB: A:48-83             ---------------------------Exon 1.12b      ----------------------------Exon 1.15       -------------------------------------Exon 1.17c  PDB: A:208-253 UniProt: 208-253   ----------------------Exon 1.19e  PDB: A:276-312            Transcript 1 (2)
                 2f7k A -10 HHHHHHEGVRTMEEECRVLSIQSHVIRGYVGNRAATFPLQVLGFEIDAVNSVQFSNHTGYAHWKGQVLNSDELQELYEGLRLNNMNKYDYVLTGYTRDKSFLAMVVDIVQELKQQNPRLVYVCDPVLGDKWDGEGSMYVPEDLLPVYKEKVVPLADIITPNQFEAELLSGRKIHSQEEALRVMDMLHSMGPDTVVITSSDLPSPQGSNYLIVLGSQRRRNPAGSVVMERIRMDIRKVDAVFVGTGDLFAAMLLAWTHKHPNNLKVACEKTVSTLHHVLQRTIQCAKAQAGEGVRPSPMQLELRMVQSKRDIEDPEIVVQATVL 312
                                    -1         9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309

Chain B from PDB  Type:PROTEIN  Length:323
 aligned with PDXK_HUMAN | O00764 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:323
                                       1                                                                                                                                                                                                                                                                                                                       
                                     - |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309   
           PDXK_HUMAN     - -----------MEEECRVLSIQSHVIRGYVGNRAATFPLQVLGFEIDAVNSVQFSNHTGYAHWKGQVLNSDELQELYEGLRLNNMNKYDYVLTGYTRDKSFLAMVVDIVQELKQQNPRLVYVCDPVLGDKWDGEGSMYVPEDLLPVYKEKVVPLADIITPNQFEAELLSGRKIHSQEEALRVMDMLHSMGPDTVVITSSDLPSPQGSNYLIVLGSQRRRNPAGSVVMERIRMDIRKVDAVFVGTGDLFAAMLLAWTHKHPNNLKVACEKTVSTLHHVLQRTIQCAKAQAGEGVRPSPMQLELRMVQSKRDIEDPEIVVQATVL 312
               SCOP domains d2f7kb_ B: automated matches                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2f7kB00 B:-10-312  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh......eeeeeeee....hhhhhhhhhhhh....eeeeeeeee..........eee.hhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhh......eeee....eee....eee.....hhhhhhhh......ee..hhhhhhhh...........hhhhhhhhh....eee..............eeeeeeeee.......eeeeeeeee........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhh........eee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) -----------Exon 1.1c  PDB: B:1-29       Exon 1.6           ----------------------------------Exon 1.10b  PDB: B:83-111    ---------------Exon 1.14  PDB: B:127-155    ---------------Exon 1.16  PDB: B:171-208             ---------------------------------------------Exon 1.18b             ------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------Exon 1.9e  PDB: B:48-83             ---------------------------Exon 1.12b      ----------------------------Exon 1.15       -------------------------------------Exon 1.17c  PDB: B:208-253 UniProt: 208-253   ----------------------Exon 1.19e  PDB: B:276-312            Transcript 1 (2)
                 2f7k B -10 HHHHHHEGVRTMEEECRVLSIQSHVIRGYVGNRAATFPLQVLGFEIDAVNSVQFSNHTGYAHWKGQVLNSDELQELYEGLRLNNMNKYDYVLTGYTRDKSFLAMVVDIVQELKQQNPRLVYVCDPVLGDKWDGEGSMYVPEDLLPVYKEKVVPLADIITPNQFEAELLSGRKIHSQEEALRVMDMLHSMGPDTVVITSSDLPSPQGSNYLIVLGSQRRRNPAGSVVMERIRMDIRKVDAVFVGTGDLFAAMLLAWTHKHPNNLKVACEKTVSTLHHVLQRTIQCAKAQAGEGVRPSPMQLELRMVQSKRDIEDPEIVVQATVL 312
                                    -1         9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Ribokinase-like (226)

Superfamily: Ribokinase-like (189)

Family: PfkB-like kinase (20)

Protein domain: automated matches (10)

Human (Homo sapiens) [TaxId: 9606] (9)

1a	d2f7ka_	A:
1b	d2f7kb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (109)

Homologous Superfamily: [code=3.40.1190.20, no name defined] (73)

Human (Homo sapiens) (10)

1a	2f7kA00	A:-10-312
1b	2f7kB00	B:-10-312

(no "Pfam Domain" information available for 2F7K)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PDXK_HUMAN | O00764)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0031403	lithium ion binding	Interacting selectively and non-covalently with lithium ions (Li+).
	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: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.
	GO:0030955	potassium ion binding	Interacting selectively and non-covalently with potassium (K+) ions.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0008478	pyridoxal kinase activity	Catalysis of the reaction: ATP + pyridoxal = ADP + pyridoxal 5'-phosphate.
	GO:0030170	pyridoxal phosphate binding	Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
	GO:0031402	sodium ion binding	Interacting selectively and non-covalently with sodium ions (Na+).
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0009443	pyridoxal 5'-phosphate salvage	Any process that generates pyridoxal 5'-phosphate, the active form of vitamin B6, from derivatives of it without de novo synthesis.
	GO:0042823	pyridoxal phosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of pyridoxal phosphate, pyridoxal phosphorylated at the hydroxymethyl group of C-5, the active form of vitamin B6.
	GO:0042816	vitamin B6 metabolic process	The chemical reactions and pathways involving any of the vitamin B6 compounds: pyridoxal, pyridoxamine and pyridoxine and the active form, pyridoxal phosphate.
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.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological 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
(no "Ligands, Modified Residues, Ions" information available for 2f7k)

	Sites
(no "Sites" information available for 2f7k)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2f7k)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit 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
	2f7k
		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
	PDXK_HUMAN \| O00764
		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)
	2.7.1.35
		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
	PDXK_HUMAN \| O00764
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	PDXK_HUMAN \| O00764	:	2ajp 2yxt 2yxu 3fhx 3fhy 3keu 4en4 4eoh

(no "Related Entries Specified in the PDB File" available for 2F7K)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (11, 22)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (23, 23)

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