2YXU - JenaLib

Asymmetric Unit (21, 21)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:118 , HOH A:1506 , HOH A:1507	BINDING SITE FOR RESIDUE MG A 1404
02	AC2	SOFTWARE	ASP A:113 , THR A:148 , THR A:186 , HOH A:1508	BINDING SITE FOR RESIDUE NA A 1406
03	AC3	SOFTWARE	ASP B:118 , HOH B:2411 , HOH B:2412	BINDING SITE FOR RESIDUE MG B 2404
04	AC4	SOFTWARE	THR B:148 , THR B:186 , HOH B:2413	BINDING SITE FOR RESIDUE NA B 2406
05	AC5	SOFTWARE	CYS A:5 , LEU A:31 , GLY A:32	BINDING SITE FOR RESIDUE PO4 A 1501
06	AC6	SOFTWARE	LEU B:31 , GLY B:32 , HIS B:246	BINDING SITE FOR RESIDUE PO4 B 1517
07	AC7	SOFTWARE	GLN B:63 , GLU B:100	BINDING SITE FOR RESIDUE PO4 B 1527
08	AC8	SOFTWARE	ASP A:113 , ASP A:118 , TYR A:127 , ASN A:150 , GLU A:153 , THR A:186 , SER A:187 , ARG A:224 , LYS A:225 , ALA A:228 , THR A:233 , GLY A:234 , LEU A:267 , HOH A:1506 , HOH A:1507 , HOH A:1510	BINDING SITE FOR RESIDUE ATP A 1410
09	AC9	SOFTWARE	ASP B:113 , ASP B:118 , TYR B:127 , THR B:148 , ASN B:150 , GLU B:153 , THR B:186 , SER B:187 , LEU B:199 , ARG B:224 , LYS B:225 , ALA B:228 , THR B:233 , GLY B:234 , LEU B:263 , LEU B:267 , HOH B:2411 , HOH B:2412 , HOH B:2419 , HOH B:2500 , HOH B:2540	BINDING SITE FOR RESIDUE ATP B 2410
10	BC1	SOFTWARE	TYR A:66 , ARG A:70 , MET A:93 , GLU A:100	BINDING SITE FOR RESIDUE MPD A 1011
11	BC2	SOFTWARE	SER A:12 , HIS A:46 , THR A:47 , TYR A:84 , HOH A:1602	BINDING SITE FOR RESIDUE MPD A 1013
12	BC3	SOFTWARE	PRO B:142 , ALA B:144 , ASP B:145 , GLY B:179 , PRO B:180 , ASP B:181 , HOH B:2438 , HOH B:2466	BINDING SITE FOR RESIDUE MPD B 1015
13	BC4	SOFTWARE	SER B:12 , HIS B:46 , THR B:47 , ASP B:235 , HOH B:2600	BINDING SITE FOR RESIDUE MPD B 1019
14	BC5	SOFTWARE	ASP B:181 , ARG B:208	BINDING SITE FOR RESIDUE MPD B 1021
15	BC6	SOFTWARE	SER B:177 , ARG B:206 , LEU B:312	BINDING SITE FOR RESIDUE MPD B 1023
16	BC7	SOFTWARE	HIS B:248 , PRO B:249 , ASN B:250 , ASN B:251 , HOH B:2546	BINDING SITE FOR RESIDUE MPD B 1025
17	BC8	SOFTWARE	GLU B:123 , GLY B:124	BINDING SITE FOR RESIDUE MPD B 1029
18	BC9	SOFTWARE	PRO A:191 , PHE B:43 , TYR B:84 , ARG B:86	BINDING SITE FOR RESIDUE MPD B 1031
19	CC1	SOFTWARE	ASP A:118 , HOH A:1507	BINDING SITE FOR RESIDUE MPD A 1037
20	CC2	SOFTWARE	ASP B:118 , HOH B:2412 , HOH B:2485 , HOH B:2500	BINDING SITE FOR RESIDUE MPD B 1039
21	CC3	SOFTWARE	PRO B:191 , HOH B:2441 , HOH B:2443	BINDING SITE FOR RESIDUE MPD B 1041

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (11, 22)

Asymmetric 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:3-29 B:3-29	27 27
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:171-207 B:171-208	37 38
1.17c	ENST00000291565	17c	ENSE00001050587	chr21:45173464-45173600	137	PDXK_HUMAN	208-253	46	2	A:212-253 B:208-253	42 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 (gaps)	37 37

Sequences/Alignments

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:306
 aligned with PDXK_HUMAN | O00764 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:310
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312
           PDXK_HUMAN     3 EECRVLSIQSHVIRGYVGNRAATFPLQVLGFEIDAVNSVQFSNHTGYAHWKGQVLNSDELQELYEGLRLNNMNKYDYVLTGYTRDKSFLAMVVDIVQELKQQNPRLVYVCDPVLGDKWDGEGSMYVPEDLLPVYKEKVVPLADIITPNQFEAELLSGRKIHSQEEALRVMDMLHSMGPDTVVITSSDLPSPQGSNYLIVLGSQRRRNPAGSVVMERIRMDIRKVDAVFVGTGDLFAAMLLAWTHKHPNNLKVACEKTVSTLHHVLQRTIQCAKAQAGEGVRPSPMQLELRMVQSKRDIEDPEIVVQATVL 312
               SCOP domains d2yxua_ A: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2yxuA00 A:3-312  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.....hhhhhhhhhhhh..eeeeeeeeee..........eee.hhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhhhhhh...eeee....eee....eee....hhhhhhhhhhhhhh.ee..hhhhhhhhhh....hhhhhhhhhhhhhhhh..eeee............eeeeeeeeee----...eeeeeeeeee.......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhh.......ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1c  PDB: A:3-29     Exon 1.6           ----------------------------------Exon 1.10b  PDB: A:83-111    ---------------Exon 1.14  PDB: A:127-155    ---------------Exon 1.16  PDB: A:171-207 [INCOMPLETE]---------------------------------------------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:212-253 UniProt: 208-253   ----------------------Exon 1.19e  PDB: A:276-312            Transcript 1 (2)
                 2yxu A   3 EECRVLSIQSHVIRGYVGNRAATFPLQVLGFEIDAVNSVQFSNHTGYAHWKGQVLNSDELQELYEGLRLNNMNKYDYVLTGYTRDKSFLAMVVDIVQELKQQNPRLVYVCDPVLGDKWDGEGSMYVPEDLLPVYKEKVVPLADIITPNQFEAELLSGRKIHSQEEALRVMDMLHSMGPDTVVITSSDLPSPQGSNYLIVLGSQRR----GSVVMERIRMDIRKVDAVFVGTGDLFAAMLLAWTHKHPNNLKVACEKTVSTLHHVLQRTIQCAKAQAGEGVRPSPMQLELRMVQSKRDIEDPEIVVQATVL 312
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202    |  212       222       232       242       252       262       272       282       292       302       312
                                                                                                                                                                                                                                      207  212

Chain B from PDB  Type:PROTEIN  Length:307
 aligned with PDXK_HUMAN | O00764 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:310
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312
           PDXK_HUMAN     3 EECRVLSIQSHVIRGYVGNRAATFPLQVLGFEIDAVNSVQFSNHTGYAHWKGQVLNSDELQELYEGLRLNNMNKYDYVLTGYTRDKSFLAMVVDIVQELKQQNPRLVYVCDPVLGDKWDGEGSMYVPEDLLPVYKEKVVPLADIITPNQFEAELLSGRKIHSQEEALRVMDMLHSMGPDTVVITSSDLPSPQGSNYLIVLGSQRRRNPAGSVVMERIRMDIRKVDAVFVGTGDLFAAMLLAWTHKHPNNLKVACEKTVSTLHHVLQRTIQCAKAQAGEGVRPSPMQLELRMVQSKRDIEDPEIVVQATVL 312
               SCOP domains d2yxub_ B: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2yxuB00 B:3-312  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                                                  CATH domains
           Pfam domains (1) PfkB-2yxuB01 B:3-283                                                                                                                                                                                                                                                                     ----------------------------- Pfam domains (1)
           Pfam domains (2) PfkB-2yxuB02 B:3-283                                                                                                                                                                                                                                                                     ----------------------------- Pfam domains (2)
         Sec.struct. author ...eeeeeeeee.....hhhhhhhhhhhh..eeeeeeeeee..........eee.hhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhhhhhh...eeee....eee....eee....hhhhhhhhhhhhhh.ee..hhhhhhhhhh....hhhhhhhhhhhhhhhh..eeee............eeeeeeeeeee.....eeeeeeeeeee.......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh---...........hhhhhhhhhh.......ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1c  PDB: B:3-29     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 (gaps)     Transcript 1 (2)
                 2yxu B   3 EECRVLSIQSHVIRGYVGNRAATFPLQVLGFEIDAVNSVQFSNHTGYAHWKGQVLNSDELQELYEGLRLNNMNKYDYVLTGYTRDKSFLAMVVDIVQELKQQNPRLVYVCDPVLGDKWDGEGSMYVPEDLLPVYKEKVVPLADIITPNQFEAELLSGRKIHSQEEALRVMDMLHSMGPDTVVITSSDLPSPQGSNYLIVLGSQRRRNPAGSVVMERIRMDIRKVDAVFVGTGDLFAAMLLAWTHKHPNNLKVACEKTVSTLHHVLQRTIQCAKAQA---VRPSPMQLELRMVQSKRDIEDPEIVVQATVL 312
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272     | 282       292       302       312
                                                                                                                                                                                                                                                                                                             278 282

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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (23, 23)

Asymmetric 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.

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	Cis Peptide Bonds
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Biological Units
	Complete Structure
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		Biological Unit 2	[ Jena3D ]

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 23)

Sites (21, 21)

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 (1, 2)

Gene Ontology (23, 23)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File