1KDR - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CYTIDINE MONOPHOSPHATE KINASE FROM E.COLI IN COMPLEX WITH ARA-CYTIDINE MONOPHOSPHATE

Authors :   T. Bertrand, P. Briozzo, L. Assairi, A. Ofiteru, N. Bucurenci, H. Munier-Lehmann, B. Golinelli-Pimpaneau, O. Barzu, A. M. Gilles

Date :   13 Nov 01 (Deposition) - 22 Jan 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Nucleotide Monophosphate Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Bertrand, P. Briozzo, L. Assairi, A. Ofiteru, N. Bucurenci, H. Munier-Lehmann, B. Golinelli-Pimpaneau, O. Barzu, A. M. Gilles
Sugar Specificity Of Bacterial Cmp Kinases As Revealed By Crystal Structures And Mutagenesis Of Escherichia Coli Enzyme.
J. Mol. Biol. V. 315 1099 2002
PubMed-ID: 11827479 | Reference-DOI: 10.1006/JMBI.2001.5286
(for further references see the PDB file header)

Molecule 1 - CYTIDYLATE KINASE
	Chains	:	A, B
	EC Number	:	2.7.4.14
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PHSP210
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	CMK
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	CYTIDINE MONOPHOSPHATE KINASE; CK; CMP KINASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	CAR	2	Mod. Residue	CYTOSINE ARABINOSE-5'-PHOSPHATE
2	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CAR	1	Mod. Residue	CYTOSINE ARABINOSE-5'-PHOSPHATE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	CAR	1	Mod. Residue	CYTOSINE ARABINOSE-5'-PHOSPHATE
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:15 , ALA A:16 , GLY A:17 , LYS A:18 , GLY A:19 , HOH A:5429	BINDING SITE FOR RESIDUE SO4 A 501
2	AC2	SOFTWARE	GLY B:15 , ALA B:16 , GLY B:17 , LYS B:18 , GLY B:19	BINDING SITE FOR RESIDUE SO4 B 601
3	AC3	SOFTWARE	GLY B:17 , THR B:20 , HIS B:51	BINDING SITE FOR RESIDUE SO4 B 602
4	AC4	SOFTWARE	SER A:36 , GLY A:37 , TYR A:40 , ARG A:41 , SER A:101 , ALA A:104 , ARG A:110 , GLY A:130 , ARG A:131 , ASP A:132 , ASP A:185 , ARG A:188 , HOH A:5429	BINDING SITE FOR RESIDUE CAR A 5407
5	AC5	SOFTWARE	SER B:36 , GLY B:37 , TYR B:40 , ARG B:41 , ALA B:104 , ARG B:110 , GLY B:130 , ARG B:131 , ASP B:132 , ASP B:185 , HOH B:6424	BINDING SITE FOR RESIDUE CAR B 6407

(no "SS Bond" information available for 1KDR)

Asymmetric Unit

No.	Residues
1	Leu A:123	-	Pro A:124
2	Leu B:123	-	Pro B:124

(no "SAP(SNP)/Variant" information available for 1KDR)

(no "PROSITE Motif" information available for 1KDR)

(no "Exon" information available for 1KDR)

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:221
 aligned with KCY_ECOLI | P0A6I0 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:221
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222 
            KCY_ECOLI     3 AIAPVITIDGPSGAGKGTLCKAMAEALQWHLLDSGAIYRVLALAALHHHVDVASEDALVPLASHLDVRFVSTNGNLEVILEGEDVSGEIRTQEVANAASQVAAFPRVREALLRRQRAFRELPGLIADGRDMGTVVFPDAPVKIFLDASSEERAHRRMLQLQEKGFSVNFERLLAEIKERDDRDRNRAVAPLVPAADALVLDSTTLSIEQVIEKALQYARQK 223
               SCOP domains d1kdra_ A: CMP kinase                                                                                                                                                                                                         SCOP domains
               CATH domains 1kdrA00 A:3-223 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhh.....hhhhhhhhhhhh.eee........eee..ee..hhhhhhhhhhhhhh...hhhhhhhhhhhhhh......eeeee............eeeeee.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh............eeee....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kdr A   3 AIAPVITIDGPSGAGKGTLCKAMAEALQWHLLDSGAIYRVLALAALHHHVDVASEDALVPLASHLDVRFVSTNGNLEVILEGEDVSGEIRTQEVANAASQVAAFPRVREALLRRQRAFRELPGLIADGRDMGTVVFPDAPVKIFLDASSEERAHRRMLQLQEKGFSVNFERLLAEIKERDDRDRNRAVAPLVPAADALVLDSTTLSIEQVIEKALQYARQK 223
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222

Chain B from PDB  Type:PROTEIN  Length:221
 aligned with KCY_ECOLI | P0A6I0 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:221
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222 
            KCY_ECOLI     3 AIAPVITIDGPSGAGKGTLCKAMAEALQWHLLDSGAIYRVLALAALHHHVDVASEDALVPLASHLDVRFVSTNGNLEVILEGEDVSGEIRTQEVANAASQVAAFPRVREALLRRQRAFRELPGLIADGRDMGTVVFPDAPVKIFLDASSEERAHRRMLQLQEKGFSVNFERLLAEIKERDDRDRNRAVAPLVPAADALVLDSTTLSIEQVIEKALQYARQK 223
               SCOP domains d1kdrb_ B: CMP kinase                                                                                                                                                                                                         SCOP domains
               CATH domains 1kdrB00 B:3-223 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                          CATH domains
           Pfam domains (1) ----------------------------------------------------------Cytidylate_kin-1kdrB01 B:61-218                                                                                                                               ----- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------Cytidylate_kin-1kdrB02 B:61-218                                                                                                                               ----- Pfam domains (2)
         Sec.struct. author ....eeeee.....hhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhh.....hhhhhhhhhhh..eeee......eeee..ee......hhhhhhhhhhhhhhhhhhh.hhhhhhh......eeeee............eeeeee.hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh............eeee....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kdr B   3 AIAPVITIDGPSGAGKGTLCKAMAEALQWHLLDSGAIYRVLALAALHHHVDVASEDALVPLASHLDVRFVSTNGNLEVILEGEDVSGEIRTQEVANAASQVAAFPRVREALLRRQRAFRELPGLIADGRDMGTVVFPDAPVKIFLDASSEERAHRRMLQLQEKGFSVNFERLLAEIKERDDRDRNRAVAPLVPAADALVLDSTTLSIEQVIEKALQYARQK 223
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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: CMP kinase (8)

Escherichia coli [TaxId: 562] (6)

1a	d1kdra_	A:
1b	d1kdrb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Escherichia coli. Organism_taxid: 562. (54)

1a	1kdrA00	A:3-223
1b	1kdrB00	B:3-223

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Cytidylate_kin (7)

Escherichia coli (strain K12) (4)

1a	Cytidylate_kin-1kdrB01	B:61-218
1b	Cytidylate_kin-1kdrB02	B:61-218

Asymmetric Unit(hide GO term definitions)

Chain A,B (KCY_ECOLI | P0A6I0)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004127	cytidylate kinase activity	Catalysis of the reaction: ATP + (d)CMP = ADP + (d)CDP.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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: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:0006139	nucleobase-containing compound metabolic process	Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
	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: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.
	GO:0006220	pyrimidine nucleotide metabolic process	The chemical reactions and pathways involving a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
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.

Asymmetric 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
		CAR	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Leu A:123 - Pro A:124	[ RasMol ]
		Leu B:123 - Pro B:124	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 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
	1kdr
		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
	KCY_ECOLI \| P0A6I0
		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)
	2.7.4.14
		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
	KCY_ECOLI \| P0A6I0
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	KCY_ECOLI \| P0A6I0	:	1cke 1kdo 1kdp 1kdt 2cmk 2fem 2feo

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (12, 12)

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