2I2B - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

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 :   CRYSTAL STRUCTURE OF LMNADK1 FROM LISTERIA MONOCYTOGENES

Authors :   G. Poncet-Montange, G. Labesse

Date :   16 Aug 06 (Deposition) - 07 Aug 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)
Biol. Unit 2: A  (2x)

Keywords :   Crystal Structure Of Lmnadk1 In Complex With Ligand Analog, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Poncet-Montange, L. Assairi, S. Arold, S. Pochet, G. Labesse
Nad Kinases Use Substrate-Assisted Catalysis For Specific Recognition Of Nad.
J. Biol. Chem. V. 282 33925 2007
PubMed-ID: 17686780 | Reference-DOI: 10.1074/JBC.M701394200

Molecule 1 - PROBABLE INORGANIC POLYPHOSPHATE/ATP-NAD KINASE 1
	Chains	:	A
	EC Number	:	2.7.1.23
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	PPNK1
	Organism Scientific	:	LISTERIA MONOCYTOGENES
	Organism Taxid	:	1639
	Synonym	:	POLYP, /ATP NAD KINASE 1

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A
Biological Unit 2 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	CC5	2	Ligand/Ion	BETA-D-ERYTHROFURANOSYL-ADENOSINE
2	CIT	1	Ligand/Ion	CITRIC ACID
3	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 1 (3, 16)

No.	Name	Count	Type	Full Name
1	CC5	8	Ligand/Ion	BETA-D-ERYTHROFURANOSYL-ADENOSINE
2	CIT	4	Ligand/Ion	CITRIC ACID
3	GOL	4	Ligand/Ion	GLYCEROL

Biological Unit 2 (3, 8)

No.	Name	Count	Type	Full Name
1	CC5	4	Ligand/Ion	BETA-D-ERYTHROFURANOSYL-ADENOSINE
2	CIT	2	Ligand/Ion	CITRIC ACID
3	GOL	2	Ligand/Ion	GLYCEROL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:122 , GLU A:123 , ASP A:150 , ALA A:162 , TYR A:163 , SER A:166 , ALA A:185 , ILE A:187 , HOH A:437 , HOH A:462	BINDING SITE FOR RESIDUE CC5 A 273
2	AC2	SOFTWARE	ASP A:45 , PHE A:74 , TYR A:75 , ASN A:122 , SER A:158 , THR A:161 , ALA A:162 , HOH A:437	BINDING SITE FOR RESIDUE CC5 A 274
3	AC3	SOFTWARE	TYR A:100 , HIS A:173 , ARG A:247 , PHE A:251 , PRO A:252 , PHE A:253 , ARG A:256 , HOH A:442	BINDING SITE FOR RESIDUE CIT A 301
4	AC4	SOFTWARE	ILE A:139 , ILE A:142 , HIS A:143 , PHE A:144 , TRP A:254 , ARG A:255 , HIS A:258	BINDING SITE FOR RESIDUE GOL A 401

(no "SS Bond" information available for 2I2B)

Asymmetric Unit

No.	Residues
1	Ser A:128	-	Ser A:129
2	Pro A:132	-	Phe A:133
3	Ser A:225	-	Ile A:226

(no "SAP(SNP)/Variant" information available for 2I2B)

(no "PROSITE Motif" information available for 2I2B)

(no "Exon" information available for 2I2B)

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:258
 aligned with NADK1_LISMO | Q8Y8D7 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:263
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260   
          NADK1_LISMO     1 MKYMITSKGDEKSDLLRLNMIAGFGEYDMEYDDVEPEIVISIGGDGTFLSAFHQYEERLDEIAFIGIHTGHLGFYADWRPAEADKLVKLLAKGEYQKVSYPLLKTTVKYGIGKKEATYLALNESTVKSSGGPFVVDVVINDIHFERFRGDGLCMSTPSGTTAYNKSLGGALMHPSIEAMQLTEMASINNRVYRTIGSPLVFPKHHVVSLQPVNDKDFQISVDHLSILHRDVQEIRYEVSAKKIHFARFRSFPFWRRVHDSFIE 263
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhhhh....ee......eeeeeehhhhhhhhhhhhhhhhhh.eeeeee..........hhhhhhhhhhhhhhh..eeeeeeeeeeeee.----..eeeee..eeeee......eeeeee..eeeeeeeeeeeeee.hhhhhhhhhhh..........eeeeeeeee...-........eeee....eeeee.....eeeee..eeeee....eeeeeeeeeeeeeee....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i2b A   1 MKYMITSKGDEKSDLLRLNMIAGFGEYDMEYDDVEPEIVISIGGDGTFLSAFHQYEERLDEIAFIGIHTGHLGFYADWRPAEADKLVKLLAKGEYQKVSYPLLKTTVKY----KEATYLALNESTVKSSGGPFVVDVVINDIHFERFRGDGLCMSTPSGTTAYNKSLGGALMHPSIEAMQLTEMASINN-VYRTIGSPLVFPKHHVVSLQPVNDKDFQISVDHLSILHRDVQEIRYEVSAKKIHFARFRSFPFWRRVHDSFIE 263
                                    10        20        30        40        50        60        70        80        90       100        |-   |   120       130       140       150       160       170       180        |-|      200       210       220       230       240       250       260   
                                                                                                                                      109  114                                                                        189 |                                                                        
                                                                                                                                                                                                                        191

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 2I2B)

(no "CATH Domain" information available for 2I2B)

(no "Pfam Domain" information available for 2I2B)

Asymmetric Unit(hide GO term definitions)

Chain A (NADK1_LISMO | Q8Y8D7)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0051287	NAD binding	Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
	GO:0003951	NAD+ kinase activity	Catalysis of the reaction: ATP + NAD(+) = ADP + 2 H(+) + NADP(+).
	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: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:0019674	NAD metabolic process	The chemical reactions and pathways involving nicotinamide adenine dinucleotide (NAD), a coenzyme present in most living cells and derived from the B vitamin nicotinic acid.
	GO:0006741	NADP biosynthetic process	The chemical reactions and pathways resulting in the formation of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; biosynthesis may be of either the oxidized form, NADP, or the reduced form, NADPH.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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
		CC5	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CIT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
		Pro A:132 - Phe A:133	[ RasMol ]
		Ser A:128 - Ser A:129	[ RasMol ]
		Ser A:225 - Ile A:226	[ 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
	2i2b
		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
	NADK1_LISMO \| Q8Y8D7
		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)
	2.7.1.23
		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
	NADK1_LISMO \| Q8Y8D7
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

2i1w	CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENES
2i29	CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENES
2i2a	CRYSTAL STRUCTURE OF LMNADK1 FROM LISTERIA MONOCYTOGENES
2i2c	CRYSTAL STRUCTURE OF LMNADK1
2i2d	CRYSTAL STRUCTURE OF LMNADK1
2i2e	CRYSTAL STRUCTURE OF LMNADK1
2i2f	CRYSTAL STRUCTURE OF LMNADK1

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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 (0, 0)

Pfam Domains (0, 0)

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