3DDI - JenaLib

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 THE MIMIVIRUS NDK +KPN-N62L-R107G TRIPLE MUTANT COMPLEXED WITH TDP

Authors :   S. Jeudy, A. Lartigue, J. M. Claverie, A. Abergel

Date :   05 Jun 08 (Deposition) - 16 Jun 09 (Release) - 25 Aug 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (3x)
Biol. Unit 2: A (1x),B (1x)

Keywords :   Tdp Phosphotransferase, Atp-Binding, Kinase, Magnesium, Metal-Binding, Nucleotide Metabolism, Nucleotide-Binding, Phosphoprotein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Jeudy, A. Lartigue, J. M. Claverie, C. Abergel
Dissecting The Unique Nucleotide Specificity Of Mimivirus Nucleoside Diphosphate Kinase.
J. Virol. V. 83 7142 2009
PubMed-ID: 19439473 | Reference-DOI: 10.1128/JVI.00511-09
(for further references see the PDB file header)

Molecule 1 - NUCLEOSIDE DIPHOSPHATE KINASE
	Chains	:	A, B
	EC Number	:	2.7.4.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDIGS02
	Expression System Strain	:	ROSETTA(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NDK, MIMI_R418
	Mutation	:	YES
	Organism Common	:	APMV
	Organism Scientific	:	ACANTHAMOEBA POLYPHAGA MIMIVIRUS
	Organism Taxid	:	212035
	Synonym	:	NDK, NDP KINASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (3x)	:	A	B
Biological Unit 2 (1x)	:	A (1x)	B (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION
2	TYD	2	Ligand/Ion	THYMIDINE-5'-DIPHOSPHATE

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	TYD	6	Ligand/Ion	THYMIDINE-5'-DIPHOSPHATE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	TYD	1	Ligand/Ion	THYMIDINE-5'-DIPHOSPHATE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC2	SOFTWARE	ASP A:119	BINDING SITE FOR RESIDUE MG A 142
2	AC3	SOFTWARE	LYS A:9 , HIS A:53 , TYR A:58 , LEU A:62 , ARG A:86 , THR A:92 , ARG A:103 , ILE A:110 , GLY A:111 , ASN A:113	BINDING SITE FOR RESIDUE TYD A 201
3	AC4	SOFTWARE	LYS B:9 , HIS B:53 , TYR B:58 , LEU B:62 , ARG B:86 , THR B:92 , ARG B:103 , ILE B:110 , ASN B:113	BINDING SITE FOR RESIDUE TYD B 201

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NDP_KINASES	PS00469	Nucleoside diphosphate kinases active site.	NDK_MIMIV	109-117	2	A:113-121 B:113-121

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NDP_KINASES	PS00469	Nucleoside diphosphate kinases active site.	NDK_MIMIV	109-117	6	A:113-121 B:113-121

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NDP_KINASES	PS00469	Nucleoside diphosphate kinases active site.	NDK_MIMIV	109-117	2	A:113-121 B:113-121

(no "Exon" information available for 3DDI)

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:133
 aligned with NDK_MIMIV | Q5UQL3 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:133
                                                                                                                    90 91 94 95                                  
                                    10        20        30        40        50        60        70        80        90  |  |  96       106       116       126   
            NDK_MIMIV     1 MQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQG--NILT--PGTIRGDLANDIRENLIHASDSEDSAVDEISIWFP 129
               SCOP domains d3ddia_ A: automated matches                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeeee.hhhhhhhhhhh..........hhhhhhh.......eee..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------NDP_KINAS------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ddi A   1 LQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDLCDFMVSGPIISIVYEGTDAISKIRRLQGNTNPLASAPGTIRGDLANDIGENLIHASDSEDSAVDEISIWFP 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain B from PDB  Type:PROTEIN  Length:133
 aligned with NDK_MIMIV | Q5UQL3 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:133
                                                                                                                    90 91 94 95                                  
                                    10        20        30        40        50        60        70        80        90  |  |  96       106       116       126   
            NDK_MIMIV     1 MQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQG--NILT--PGTIRGDLANDIRENLIHASDSEDSAVDEISIWFP 129
               SCOP domains d3ddib_ B: automated matches                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeeee.hhhhhhhhhhh..........hhhhhhh.......eee..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------NDP_KINAS------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ddi B   1 LQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDLCDFMVSGPIISIVYEGTDAISKIRRLQGNTNPLASAPGTIRGDLANDIGENLIHASDSEDSAVDEISIWFP 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

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) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: Nucleoside diphosphate kinase, NDK (129)

Family: Nucleoside diphosphate kinase, NDK (112)

Protein domain: automated matches (46)

Acanthamoeba polyphaga mimivirus [TaxId: 212035] (23)

1a	d3ddia_	A:
1b	d3ddib_	B:

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (NDK_MIMIV | Q5UQL3)

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:0004550	nucleoside diphosphate kinase activity	Catalysis of the reaction: ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.
	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:0006241	CTP biosynthetic process	The chemical reactions and pathways resulting in the formation of CTP, cytidine 5'-triphosphate.
	GO:0006183	GTP biosynthetic process	The chemical reactions and pathways resulting in the formation of GTP, guanosine triphosphate.
	GO:0006228	UTP biosynthetic process	The chemical reactions and pathways resulting in the formation of UTP, uridine (5'-)triphosphate.
	GO:0006165	nucleoside diphosphate phosphorylation	The process of introducing a phosphate group into a nucleoside diphosphate to produce a nucleoside triphosphate.
	GO:0009117	nucleotide metabolic process	The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
	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 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
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		TYD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ddi)

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
	3ddi
		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
	NDK_MIMIV \| Q5UQL3
		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)
	2.7.4.6
		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
	NDK_MIMIV \| Q5UQL3
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

2b8p	CRYSTAL STRUCTURE OF MIMIVIRUS NDK
2b8q	CRYSTAL STRUCTURE OF MIMIVIRUS NDK COMPLEXED WITH TDP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

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