2B8Q - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   X-RAY STRUCTURE OF ACANTHAMOEBA PLOYPHAGA MIMIVIRUS NUCLEOSIDE DIPHOSPHATE KINASE COMPLEXED WITH TDP

Authors :   S. Jeudy, J. M. Claverie, C. Abergel

Date :   10 Oct 05 (Deposition) - 15 Nov 05 (Release) - 25 Aug 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,C,E  (2x)
Biol. Unit 2: B,D,F  (2x)

Keywords :   Ndk, Tdp, Phosphotranferase, 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 - PROBABLE NUCLEOSIDE DIPHOSPHATE KINASE
	Chains	:	A, B, C, D, E, F
	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
	Organism Scientific	:	MIMIVIRUS
	Organism Taxid	:	315393
	Synonym	:	NDK, NDP KINASE

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (2x)	:	A		C		E
Biological Unit 2 (2x)	:		B		D		F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 13)

No.	Name	Count	Type	Full Name
1	MG	6	Ligand/Ion	MAGNESIUM ION
2	PO4	1	Ligand/Ion	PHOSPHATE ION
3	TYD	6	Ligand/Ion	THYMIDINE-5'-DIPHOSPHATE

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	PO4	2	Ligand/Ion	PHOSPHATE ION
3	TYD	6	Ligand/Ion	THYMIDINE-5'-DIPHOSPHATE

Biological Unit 2 (1, 6)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	PO4	-1	Ligand/Ion	PHOSPHATE ION
3	TYD	6	Ligand/Ion	THYMIDINE-5'-DIPHOSPHATE

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYD A:160	BINDING SITE FOR RESIDUE MG A 201
02	AC2	SOFTWARE	TYD B:161	BINDING SITE FOR RESIDUE MG B 202
03	AC3	SOFTWARE	TYD C:162	BINDING SITE FOR RESIDUE MG C 203
04	AC4	SOFTWARE	ARG D:86 , ASP D:115 , TYD D:163	BINDING SITE FOR RESIDUE MG D 204
05	AC5	SOFTWARE	ARG F:86 , ASP F:115 , TYD F:165	BINDING SITE FOR RESIDUE MG F 205
06	AC6	SOFTWARE	TYD E:164	BINDING SITE FOR RESIDUE MG E 206
07	AC7	SOFTWARE	LYS A:9 , HIS A:53 , TYR A:58 , ASN A:62 , ARG A:86 , ARG A:99 , ILE A:106 , ARG A:107 , ASN A:109 , MG A:201	BINDING SITE FOR RESIDUE TYD A 160
08	AC8	SOFTWARE	LYS B:9 , TYR B:50 , HIS B:53 , TYR B:58 , ASN B:62 , ARG B:86 , ARG B:99 , ILE B:106 , ARG B:107 , ASN B:109 , MG B:202 , HOH B:210	BINDING SITE FOR RESIDUE TYD B 161
09	AC9	SOFTWARE	LYS C:9 , TYR C:50 , HIS C:53 , TYR C:58 , ASN C:62 , ARG C:86 , ARG C:99 , ILE C:106 , ARG C:107 , ASN C:109 , MG C:203 , HOH C:1029	BINDING SITE FOR RESIDUE TYD C 162
10	BC1	SOFTWARE	LYS D:9 , TYR D:50 , HIS D:53 , TYR D:58 , ASN D:62 , ARG D:86 , ARG D:99 , ILE D:106 , ARG D:107 , ASN D:109 , MG D:204	BINDING SITE FOR RESIDUE TYD D 163
11	BC2	SOFTWARE	LYS E:9 , HIS E:53 , TYR E:58 , ASN E:62 , ARG E:86 , ARG E:99 , ILE E:106 , ARG E:107 , ASN E:109 , MG E:206 , HOH E:214	BINDING SITE FOR RESIDUE TYD E 164
12	BC3	SOFTWARE	LYS F:9 , TYR F:50 , HIS F:53 , TYR F:58 , ASN F:62 , ARG F:86 , ARG F:99 , ILE F:106 , ARG F:107 , ASN F:109 , MG F:205	BINDING SITE FOR RESIDUE TYD F 165

(no "SS Bond" information available for 2B8Q)

(no "Cis Peptide Bond" information available for 2B8Q)

(no "SAP(SNP)/Variant" information available for 2B8Q)

Asymmetric Unit (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:109-117 B:109-117 C:109-117 D:109-117 E:109-117 F:109-117

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:109-117 - C:109-117 - E:109-117 -

Biological Unit 2 (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	- B:109-117 - D:109-117 - F:109-117

(no "Exon" information available for 2B8Q)

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
                              1                                                                                                                                  
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128   
            NDK_MIMIV     - --MQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPET 131
               SCOP domains ---d2b8qa1 A:2-129 Nucleoside diphosphate kinase, NDK                                                                              -- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeeeeehhhhhhhhhhh......hhhhhhh.......eee..hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------NDP_KINAS-------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b8q A  -1 AGLQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPET 131
                                     8        18        28        38        48        58        68        78        88        98       108       118       128

Chain B from PDB  Type:PROTEIN  Length:130
 aligned with NDK_MIMIV | Q5UQL3 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:130
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
            NDK_MIMIV     1 MQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPE 130
               SCOP domains -d2b8qb1 B:2-129 Nucleoside diphosphate kinase, NDK                                                                              - SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhh.hhhhhhhhhhh...eeeeeeee...hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeeee.hhhhhhhhhhh......hhhhhhh.......eee..hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------NDP_KINAS------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b8q B   1 LQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPE 130
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain C from PDB  Type:PROTEIN  Length:132
 aligned with NDK_MIMIV | Q5UQL3 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:132
                             1                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129  
            NDK_MIMIV     - -MQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPET 131
               SCOP domains --d2b8qc1 C:2-129 Nucleoside diphosphate kinase, NDK                                                                              -- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhh.hhhhhhhhhhh...eeeeeeee...hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeeeeehhhhhhhhhhh......hhhhhhh.......eee..hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------NDP_KINAS-------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2b8q C   0 GLQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPET 131
                                     9        19        29        39        49        59        69        79        89        99       109       119       129

Chain D from PDB  Type:PROTEIN  Length:132
 aligned with NDK_MIMIV | Q5UQL3 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:132
                             1                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129  
            NDK_MIMIV     - -MQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPET 131
               SCOP domains --d2b8qd1 D:2-129 Nucleoside diphosphate kinase, NDK                                                                              -- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhhh...hhhhhhhhhhh..eeeeeeeeehhhhhhhhhhh......hhhhhhh.......eee..hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------NDP_KINAS-------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2b8q D   0 GLQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPET 131
                                     9        19        29        39        49        59        69        79        89        99       109       119       129

Chain E from PDB  Type:PROTEIN  Length:132
 aligned with NDK_MIMIV | Q5UQL3 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:132
                             1                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129  
            NDK_MIMIV     - -MQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPET 131
               SCOP domains --d2b8qe1 E:2-129 Nucleoside diphosphate kinase, NDK                                                                              -- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhh.hhhhhhhhhhh...eeeeeeee...hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeeeeehhhhhhhhhhh......hhhhhhh.......eee..hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------NDP_KINAS-------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2b8q E   0 GLQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFPET 131
                                     9        19        29        39        49        59        69        79        89        99       109       119       129

Chain F from PDB  Type:PROTEIN  Length:130
 aligned with NDK_MIMIV | Q5UQL3 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:130
                             1                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129
            NDK_MIMIV     - -MQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFP 129
               SCOP domains --d2b8qf1 F:2-129 Nucleoside diphosphate kinase, NDK                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeehhhhhhhhhhh......hhhhhhh.......eee..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------NDP_KINAS------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b8q F   0 GLQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQHYKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIRGDLANDIRENLIHASDSEDSAVDEISIWFP 129
                                     9        19        29        39        49        59        69        79        89        99       109       119       129

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: Nucleoside diphosphate kinase, NDK (66)

Mimivirus [TaxId: 315393] (2)

1a	d2b8qa1	A:2-129
1b	d2b8qb1	B:2-129
1c	d2b8qc1	C:2-129
1d	d2b8qd1	D:2-129
1e	d2b8qe1	E:2-129
1f	d2b8qf1	F:2-129

(no "CATH Domain" information available for 2B8Q)

(no "Pfam Domain" information available for 2B8Q)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (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.

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2b8p	CRYSTAL STRUCTURE OF ACANTHAMOEBA POLYPHAGA MIMIVIRUS NDK

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 13)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 6)

Exons (0, 0)

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SCOP Domains (1, 6)

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