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Title :   THE STRUCTURE OF HCINAP-DADP COMPLEX AT 2.0 ANGSTROMS RESOLUTION

Authors :   S. E. Zographos, C. E. Drakou, D. D. Leonidas

Date :   02 Aug 09 (Deposition) - 06 Oct 10 (Release) - 18 Jan 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

Keywords :   Alpha And Beta Proteins (A/B), Protein Binding, Transferase, Phosphotransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. E. Drakou, A. Malekkou, J. M. Hayes, C. W. Lederer, D. D. Leonidas, N. G. Oikonomakos, A. I. Lamond, N. Santama, S. E. Zographos
Hcinap Is An Atypical Mammalian Nuclear Adenylate Kinase With An Atpase Motif: Structural And Functional Studies.
Proteins V. 80 206 2012
PubMed-ID: 22038794 | Reference-DOI: 10.1002/PROT.23186

Molecule 1 - COILIN-INTERACTING NUCLEAR ATPASE PROTEIN
	Chains	:	A
	EC Number	:	2.7.4.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-3
	Expression System Strain	:	B834(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CINAP, TAF9, HCG_37060
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	COILIN-INTERACTING NULCEAR ATPASE PROTEIN, TAF9 RNA POLYMERASE II, TATA BOX BINDING PROTEIN (TBP)-ASSOCIATED FACTOR, 32KDA, ISOFORM CRA_B, HUMAN ADENYLATE KINASE 6

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 7)

No.	Name	Count	Type	Full Name
1	DAT	1	Ligand/Ion	2'-DEOXYADENOSINE-5'-DIPHOSPHATE
2	DTV	1	Ligand/Ion	(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
3	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:40 , PRO A:85 , GLU A:86 , ARG A:87 , HOH A:336	BINDING SITE FOR RESIDUE DTV A 173
2	AC2	SOFTWARE	ARG A:96 , GLN A:126 , GLN A:143 , PRO A:145 , GLU A:164 , GLN A:165 , LYS A:168 , HOH A:242 , HOH A:261 , HOH A:316	BINDING SITE FOR RESIDUE EPE A 174
3	AC3	SOFTWARE	GLY A:13 , VAL A:14 , GLY A:15 , LYS A:16 , THR A:17 , THR A:18 , ARG A:105 , ARG A:109 , SER A:146 , ASN A:147 , LYS A:148 , PRO A:149 , LEU A:152 , HOH A:208 , HOH A:213 , HOH A:223 , HOH A:224 , HOH A:227 , HOH A:231	BINDING SITE FOR RESIDUE DAT A 175
4	AC4	SOFTWARE	GLU A:138 , HOH A:186 , HOH A:311 , HOH A:348	BINDING SITE FOR RESIDUE SO4 A 176
5	AC5	SOFTWARE	ILE A:91 , PHE A:93 , TRP A:162 , HOH A:244	BINDING SITE FOR RESIDUE SO4 A 177
6	AC6	SOFTWARE	TYR A:129 , VAL A:141 , HIS A:142 , GLN A:143 , HOH A:361 , HOH A:381	BINDING SITE FOR RESIDUE SO4 A 178
7	AC7	SOFTWARE	ASN A:112 , GLU A:113 , HOH A:199	BINDING SITE FOR RESIDUE SO4 A 179

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

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

(no "SAP(SNP)/Variant" information available for 3IIM)

(no "PROSITE Motif" information available for 3IIM)

Asymmetric/Biological Unit (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2b	ENST00000380822	2b	ENSE00001867641	chr5:68665369-68665290	80	KAD6_HUMAN	1-10	10	1	A:1-10	10
1.5b	ENST00000380822	5b	ENSE00001756532	chr5:68662422-68662330	93	KAD6_HUMAN	10-41	32	1	A:10-41	32
1.7	ENST00000380822	7	ENSE00001486415	chr5:68651780-68651722	59	KAD6_HUMAN	41-60	20	1	A:41-60	20
1.8	ENST00000380822	8	ENSE00001486410	chr5:68651621-68651476	146	KAD6_HUMAN	61-109	49	1	A:61-109	49
1.9d	ENST00000380822	9d	ENSE00001549839	chr5:68648080-68646811	1270	KAD6_HUMAN	109-172	64	1	A:109-172	64

Asymmetric/Biological Unit

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	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:174
 aligned with KAD6_HUMAN | Q9Y3D8 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:174
                              1                                                                                                                                                                           
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168    
           KAD6_HUMAN     - --MLLPNILLTGTPGVGKTTLGKELASKSGLKYINVGDLAREEQLYDGYDEEYDCPILDEDRVVDELDNQMREGGVIVDYHGCDFFPERWFHIVFVLRTDTNVLYERLETRGYNEKKLTDNIQCEIFQVLYEEATASYKEEIVHQLPSNKPEELENNVDQILKWIEQWIKDHNS 172
               SCOP domains d3iima_ A: automated matches                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeee.....hhhhhhhhhhhhhh.eeeehhhhhhhh..eeeee....eeeehhhhhhhhhhhhhhhh.eeee.......hhhhh.eeeeee.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) --Exon 1.2b ------------------------------Exon 1.7            Exon 1.8  PDB: A:61-109 UniProt: 61-109          --------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.5b  PDB: A:10-41         -------------------------------------------------------------------Exon 1.9d  PDB: A:109-172 UniProt: 109-172                       Transcript 1 (2)
                 3iim A  -1 EFMLLPNILLTGTPGVGKTTLGKELASKSGLKYINVGDLAREEQLYDGYDEEYDCPILDEDRVVDELDNQMREGGVIVDYHGCDFFPERWFHIVFVLRTDTNVLYERLETRGYNEKKLTDNIQCEIFQVLYEEATASYKEEIVHQLPSNKPEELENNVDQILKWIEQWIKDHNS 172
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168

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 '\|'

Asymmetric/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: Nucleotide and nucleoside kinases (231)

Protein domain: automated matches (25)

Human (Homo sapiens) [TaxId: 9606] (7)

d3iima_

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (KAD6_HUMAN | Q9Y3D8)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016887	ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
	GO:0004017	adenylate kinase activity	Catalysis of the reaction: ATP + AMP = 2 ADP.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0050145	nucleoside phosphate kinase activity	Catalysis of the reaction: ATP + nucleoside phosphate = ADP + nucleoside diphosphate.
	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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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:0015949	nucleobase-containing small molecule interconversion	The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
	GO:0046940	nucleoside monophosphate phosphorylation	The process of introducing one or more phosphate groups into a nucleoside monophosphate to produce a polyphosphorylated nucleoside.
	GO:0046939	nucleotide phosphorylation	The process of introducing one or more phosphate groups into a nucleotide to produce a phosphorylated nucleoside.
	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.
cellular component
	GO:0015030	Cajal body	A class of nuclear body, first seen after silver staining by Ramon y Cajal in 1903, enriched in small nuclear ribonucleoproteins, and certain general RNA polymerase II transcription factors; ultrastructurally, they appear as a tangle of coiled, electron-dense threads roughly 0.5 micrometers in diameter; involved in aspects of snRNP biogenesis; the protein coilin serves as a marker for Cajal bodies. Some argue that Cajal bodies are the sites for preassembly of transcriptosomes, unitary particles involved in transcription and processing of RNA.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	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
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	Cis Peptide Bonds
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	KAD6_HUMAN \| Q9Y3D8	:	1rkb 3iij 3iik 3iil 5jzv

1rkb	THE STRUCTURE OF ADRENAL GLAND PROTEIN AD-004
3iij	THE STRUCTURE OF HCINAP-ADP COMPLEX AT 1.76 ANGSTROMS RESOLUTION.
3iik	THE STRUCTURE OF HCINAP-SO4 COMPLEX AT 1.95 ANGSTROMS RESOLUTION
3iil	THE STRUCTURE OF HCINAP-MGADP-PI COMPLEX AT 2.0 ANGSTROMS RESOLUTION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Exons (5, 5)

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SCOP Domains (1, 1)

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Gene Ontology (17, 17)

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