2E9Y - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PROJECT APE1968 FROM AEROPYRUM PERNIX K1

Authors :   K. Shimizu, Riken Structural Genomics/Proteomics Initiative (R

Date :   29 Jan 07 (Deposition) - 31 Jul 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Transferase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Shimizu, N. Kunishima
Crystal Structure Of Project Ape1968 From Aeropyrum Pernix K1
To Be Published
PubMed: search

Molecule 1 - CARBAMATE KINASE
	Chains	:	A, B
	EC Number	:	2.7.2.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET 21A
	Expression System Strain	:	BL-21 CODONPLUS (DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	AEROPYRUM PERNIX
	Organism Taxid	:	272557
	Strain	:	K1

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2E9Y)

(no "Site" information available for 2E9Y)

(no "SS Bond" information available for 2E9Y)

(no "Cis Peptide Bond" information available for 2E9Y)

(no "SAP(SNP)/Variant" information available for 2E9Y)

(no "PROSITE Motif" information available for 2E9Y)

(no "Exon" information available for 2E9Y)

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:313
 aligned with Q9YAH1_AERPE | Q9YAH1 from UniProtKB/TrEMBL  Length:316

    Alignment length:313
                                    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       313   
         Q9YAH1_AERPE     4 GRLAVIALGGNAIAGPGMDVSVESQTAAVKRASSIIADVLADGWRSVITHGNGPQVGYLSEAFEALPPERPRQPLYIATAMTQAWIGLLLKHSLEEELRRRGLNVLVPVVISRVLVDVSDPSFNNPSKPVGPIYGREEAEELSRRYGWVFKRDPRGGFRRVVPSPRPVSIVDRDLIAEASAESPAVVALGGGGVPVVERPGGVLEPVEAVVDKDLASSLLATQLNADLLVILTDVPGVAVNYGREGERWLRRAAASELKKYLREGHFPPGSMGPKVEAAISFVERTGKPAVIGSLEEARQVLSLQAGTVVMLG 316
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2e9yA00 A:4-316  [code=3.40.1160.10, no name defined]                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhhhhh......hhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......ee..eeee...hhhhh...eeeeeeehhhhhhhhhhhhh.eeee.....eeeee....eeee.hhhhhhhhhhhh.eeee.hhhheeeee.....eee.....hhhhhhhhhhhhh...eeeeee.....ee.......ee..eeehhhhhhhhhh......hhhhhhhhhhhhhhhhh..eeeee..hhhhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e9y A   4 GRLAVIALGGNAIAGPGMDVSVESQTAAVKRASSIIADVLADGWRSVITHGNGPQVGYLSEAFEALPPERPRQPLYIATAMTQAWIGLLLKHSLEEELRRRGLNVLVPVVISRVLVDVSDPSFNNPSKPVGPIYGREEAEELSRRYGWVFKRDPRGGFRRVVPSPRPVSIVDRDLIAEASAESPAVVALGGGGVPVVERPGGVLEPVEAVVDKDLASSLLATQLNADLLVILTDVPGVAVNYGREGERWLRRAAASELKKYLREGHFPPGSMGPKVEAAISFVERTGKPAVIGSLEEARQVLSLQAGTVVMLG 316
                                    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       313

Chain B from PDB  Type:PROTEIN  Length:312
 aligned with Q9YAH1_AERPE | Q9YAH1 from UniProtKB/TrEMBL  Length:316

    Alignment length:312
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314  
         Q9YAH1_AERPE     5 RLAVIALGGNAIAGPGMDVSVESQTAAVKRASSIIADVLADGWRSVITHGNGPQVGYLSEAFEALPPERPRQPLYIATAMTQAWIGLLLKHSLEEELRRRGLNVLVPVVISRVLVDVSDPSFNNPSKPVGPIYGREEAEELSRRYGWVFKRDPRGGFRRVVPSPRPVSIVDRDLIAEASAESPAVVALGGGGVPVVERPGGVLEPVEAVVDKDLASSLLATQLNADLLVILTDVPGVAVNYGREGERWLRRAAASELKKYLREGHFPPGSMGPKVEAAISFVERTGKPAVIGSLEEARQVLSLQAGTVVMLG 316
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2e9yB00 B:5-316  [code=3.40.1160.10, no name defined]                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.hhhhh.......hhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......ee..eee....hhhhh...eeeeeeehhhhhhhhhhhhh.eeee.....eeeee......ee.hhhhhhhhhhhh.eeee.hhhheeeee.....eee.....hhhhhhhhhhhhh...eeeeee..................eeehhhhhhhhhh......hhhhhhhhhhhhhhhhh..eeeee..hhhhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2e9y B   5 RLAVIALGGNAIAGPGMDVSVESQTAAVKRASSIIADVLADGWRSVITHGNGPQVGYLSEAFEALPPERPRQPLYIATAMTQAWIGLLLKHSLEEELRRRGLNVLVPVVISRVLVDVSDPSFNNPSKPVGPIYGREEAEELSRRYGWVFKRDPRGGFRRVVPSPRPVSIVDRDLIAEASAESPAVVALGGGGVPVVERPGGVLEPVEAVVDKDLASSLLATQLNADLLVILTDVPGVAVNYGREGERWLRRAAASELKKYLREGHFPPGSMGPKVEAAISFVERTGKPAVIGSLEEARQVLSLQAGTVVMLG 316
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314

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 2E9Y)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Carbamate kinase (24)

Homologous Superfamily: [code=3.40.1160.10, no name defined] (24)

Aeropyrum pernix k1. Organism_taxid: 272557. Strain: k1. (1)

1a	2e9yB00	B:5-316
1b	2e9yA00	A:4-316

(no "Pfam Domain" information available for 2E9Y)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q9YAH1_AERPE | Q9YAH1)

molecular function
	GO:0008804	carbamate kinase activity	Catalysis of the reaction: ATP + NH3 + CO2 = ADP + carbamoyl phosphate.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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:0006525	arginine metabolic process	The chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
	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.

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 2e9y)

	Sites
(no "Sites" information available for 2e9y)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2e9y)

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
	2e9y
		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
	Q9YAH1_AERPE \| Q9YAH1
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	2.7.2.2
		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
	Q9YAH1_AERPE \| Q9YAH1
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 2E9Y)

(no "Related Entries Specified in the PDB File" available for 2E9Y)

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 (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

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