1YGK - JenaLib

Title :   CRYSTAL STRUCTURE OF PYRIDOXAL KINASE IN COMPLEX WITH ROSCOVITINE AND DERIVATIVES

Authors :   L. Tang, M. -H. Li, P. Cao, F. Wang, W. -R. Chang, S. Bach, J. Reinhardt, Y. Ferandin, M. Koken, H. Galons, Y. Wan, N. Gray, L. Meijer, T. Jiang, D. -C. Liang

Date :   05 Jan 05 (Deposition) - 05 Jul 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym./Biol. Unit : A

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

Reference :   L. Tang, M. -H. Li, P. Cao, F. Wang, W. -R. Chang, S. Bach, J. Reinhardt, Y. Ferandin, H. Galons, Y. Wan, N. Gray, L. Meijer, T. Jiang, D. -C. Liang
Crystal Structure Of Pyridoxal Kinase In Complex With Roscovitine And Derivatives
J. Biol. Chem. V. 280 31220 2005
PubMed-ID: 15985434 | Reference-DOI: 10.1074/JBC.M500805200
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

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

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
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Chain A from PDB  Type:PROTEIN  Length:309
 aligned with PDXK_SHEEP | P82197 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:309
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303         
           PDXK_SHEEP     4 ECRVLSIQSHVVRGYVGNRAATFPLQVLGFEVDAVNSVQFSNHTGYSHWKGQVLNSDELQELYDGLKLNHVNQYDYVLTGYTRDKSFLAMVVDIVQELKQQNPRLVYVCDPVMGDQRNGEGAMYVPDDLLPVYREKVVPVADIITPNQFEAELLTGRKIHSQEEALEVMDMLHSMGPDTVVITSSNLLSPRGSDYLMALGSQRTRAPDGSVVTQRIRMEMHKVDAVFVGTGDLFAAMLLAWTHKHPNNLKVACEKTVSAMHHVLQRTIKCAKAKSGEGVKPSPAQLELRMVQSKKDIESPEIVVQATVL 312
               SCOP domains d1ygka_ A: Pyridoxal kinase                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1ygkA00 A:4-312  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains PfkB-1ygkA01 A:4-284                                                                                                                                                                                                                                                                     ---------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee.....hhhhhhhhhhhh..eeeeeeeeee..........eee.hhhhhhhhhhhhhhh.......eee....hhhhhhhhhhhhhhhhhhh....eee................hhhhhhhhhhh......ee..hhhhhhhhhh....hhhhhhhhhhhhhh.....eee.............ee.eee.............ee..ee........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhh..hhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ygk A   4 ECRVLSIQSHVVRGYVGNRAATFPLQVLGFEVDAVNSVQFSNHTGYSHWKGQVLNSDELQELYDGLKLNHVNQYDYVLTGYTRDKSFLAMVVDIVQELKQQNPRLVYVCDPVMGDQRNGEGAMYVPDDLLPVYREKVVPVADIITPNQFEAELLTGRKIHSQEEALEVMDMLHSMGPDTVVITSSNLLSPRGSDYLMALGSQRTRAPDGSVVTQRIRMEMHKVDAVFVGTGDLFAAMLLAWTHKHPNNLKVACEKTVSAMHHVLQRTIKCAKAKSGEGVKPSPAQLELRMVQSKKDIESPEIVVQATVL 312
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303

Legend:		→ Mismatch	(orange background)
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	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, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PDXK_SHEEP | P82197)

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: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:0008478	pyridoxal kinase activity	Catalysis of the reaction: ATP + pyridoxal = ADP + pyridoxal 5'-phosphate.
	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.
biological process
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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