3PRV - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   NUCLEOSIDE DIPHOSPHATE KINASE B FROM TRYPANOSOMA CRUZI

Authors :   T. A. C. B. Souza, D. M. Trindade, C. C. C. Tonoli, C. R. Santos, A. H. C. Oli M. T. Murakami

Date :   30 Nov 10 (Deposition) - 18 May 11 (Release) - 29 Jun 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.69

Chains :   Asym./Biol. Unit : A,B,C,D,E,F

Keywords :   Nucleoside Diphosphate Kinase B, Trypanosomatids, Alpha-Beta-Alpha Fold, Transferase, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. A. Souza, D. M. Trindade, C. C. Tonoli, C. R. Santos, R. J. Ward, R. K. Arni, A. H. Oliveira, M. T. Murakami
Molecular Adaptability Of Nucleoside Diphosphate Kinase B From Trypanosomatid Parasites: Stability, Oligomerization And Structural Determinants Of Nucleotide Binding.
Mol Biosyst V. 7 2189 2011
PubMed-ID: 21528129 | Reference-DOI: 10.1039/C0MB00307G

Molecule 1 - 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	:	PET28A
	Expression System Strain	:	DELTA SLYD
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	TRYPANOSOMA CRUZI
	Organism Taxid	:	5693
	Strain	:	CL BRENER

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3PRV)

(no "Site" information available for 3PRV)

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

Asymmetric/Biological Unit

No.	Residues
1	Leu A:54	-	Ala A:55
2	Phe A:59	-	Tyr A:60
3	Ala B:55	-	Ser B:56
4	Lys B:57	-	Pro B:58
5	Thr C:2	-	Ser C:3
6	Leu D:54	-	Ala D:55
7	Gly D:81	-	Val D:82
8	Thr E:2	-	Ser E:3
9	Thr F:2	-	Ser F:3
10	Gln F:48	-	Gln F:49
11	Gln F:49	-	His F:50
12	Asp F:53	-	Leu F:54
13	Ser F:56	-	Lys F:57

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

(no "PROSITE Motif" information available for 3PRV)

(no "Exon" information available for 3PRV)

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:150
 aligned with Q4E256_TRYCC | Q4E256 from UniProtKB/TrEMBL  Length:153

    Alignment length:150
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151
         Q4E256_TRYCC     2 TSERTFIAVKPDGVQRCLVGEIIQRFEKKGYKLVALKMLQPSAEQAQQHYIDLASKPFYKDLVAYFSSGPIVGMVWEGKGVVKGGRVLLGATNPADSLPGTIRGDFAVDVGRNVCHGSDSVDSAKREIAFWFKPEELVNWTSHSVKQVYE 151
               SCOP domains d3prva_ A: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhh.......hhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3prv A   2 TSERTFIAVKPDGVQRCLVGEIIQRFEKKGYKLVALKMLQPSAEQAQQHYIDLASKPFYKDLVAYFSSGPIVGMVWEGKGVVKGGRVLLGATNPADSLPGTIRGDFAVDVGRNVCHGSDSVDSAKREIAFWFKPEELVNWTSHSVKQVYE 151
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain B from PDB  Type:PROTEIN  Length:151
 aligned with Q4E256_TRYCC | Q4E256 from UniProtKB/TrEMBL  Length:153

    Alignment length:151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 
         Q4E256_TRYCC     1 MTSERTFIAVKPDGVQRCLVGEIIQRFEKKGYKLVALKMLQPSAEQAQQHYIDLASKPFYKDLVAYFSSGPIVGMVWEGKGVVKGGRVLLGATNPADSLPGTIRGDFAVDVGRNVCHGSDSVDSAKREIAFWFKPEELVNWTSHSVKQVYE 151
               SCOP domains d3prvb_ B: automated matches                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhh.......hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3prv B   1 MTSERTFIAVKPDGVQRCLVGEIIQRFEKKGYKLVALKMLQPSAEQAQQHYIDLASKPFYKDLVAYFSSGPIVGMVWEGKGVVKGGRVLLGATNPADSLPGTIRGDFAVDVGRNVCHGSDSVDSAKREIAFWFKPEELVNWTSHSVKQVYE 151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain C from PDB  Type:PROTEIN  Length:151
 aligned with Q4E256_TRYCC | Q4E256 from UniProtKB/TrEMBL  Length:153

    Alignment length:151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 
         Q4E256_TRYCC     1 MTSERTFIAVKPDGVQRCLVGEIIQRFEKKGYKLVALKMLQPSAEQAQQHYIDLASKPFYKDLVAYFSSGPIVGMVWEGKGVVKGGRVLLGATNPADSLPGTIRGDFAVDVGRNVCHGSDSVDSAKREIAFWFKPEELVNWTSHSVKQVYE 151
               SCOP domains d3prvc_ C: automated matches                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee..hhhhhhhhh........hhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3prv C   1 MTSERTFIAVKPDGVQRCLVGEIIQRFEKKGYKLVALKMLQPSAEQAQQHYIDLASKPFYKDLVAYFSSGPIVGMVWEGKGVVKGGRVLLGATNPADSLPGTIRGDFAVDVGRNVCHGSDSVDSAKREIAFWFKPEELVNWTSHSVKQVYE 151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain D from PDB  Type:PROTEIN  Length:150
 aligned with Q4E256_TRYCC | Q4E256 from UniProtKB/TrEMBL  Length:153

    Alignment length:150
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151
         Q4E256_TRYCC     2 TSERTFIAVKPDGVQRCLVGEIIQRFEKKGYKLVALKMLQPSAEQAQQHYIDLASKPFYKDLVAYFSSGPIVGMVWEGKGVVKGGRVLLGATNPADSLPGTIRGDFAVDVGRNVCHGSDSVDSAKREIAFWFKPEELVNWTSHSVKQVYE 151
               SCOP domains d3prvd_ D: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhh...........hhhhhh...eeeeeee...hhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhh...........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3prv D   2 TSERTFIAVKPDGVQRCLVGEIIQRFEKKGYKLVALKMLQPSAEQAQQHYIDLASKPFYKDLVAYFSSGPIVGMVWEGKGVVKGGRVLLGATNPADSLPGTIRGDFAVDVGRNVCHGSDSVDSAKREIAFWFKPEELVNWTSHSVKQVYE 151
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain E from PDB  Type:PROTEIN  Length:140
 aligned with Q4E256_TRYCC | Q4E256 from UniProtKB/TrEMBL  Length:153

    Alignment length:150
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151
         Q4E256_TRYCC     2 TSERTFIAVKPDGVQRCLVGEIIQRFEKKGYKLVALKMLQPSAEQAQQHYIDLASKPFYKDLVAYFSSGPIVGMVWEGKGVVKGGRVLLGATNPADSLPGTIRGDFAVDVGRNVCHGSDSVDSAKREIAFWFKPEELVNWTSHSVKQVYE 151
               SCOP domains d3prve_ E: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhh..----------............eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.......eee..hhhhhhhhhhhhh...........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3prv E   2 TSERTFIAVKPDGVQRCLVGEIIQRFEKKGYKLVALKMLQPSAEQAQQ----------YKDLVAYFSSGPIVGMVWEGKGVVKGGRVLLGATNPADSLPGTIRGDFAVDVGRNVCHGSDSVDSAKREIAFWFKPEELVNWTSHSVKQVYE 151
                                    11        21        31        41       | -        61        71        81        91       101       111       121       131       141       151
                                                                          49         60

Chain F from PDB  Type:PROTEIN  Length:150
 aligned with Q4E256_TRYCC | Q4E256 from UniProtKB/TrEMBL  Length:153

    Alignment length:150
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151
         Q4E256_TRYCC     2 TSERTFIAVKPDGVQRCLVGEIIQRFEKKGYKLVALKMLQPSAEQAQQHYIDLASKPFYKDLVAYFSSGPIVGMVWEGKGVVKGGRVLLGATNPADSLPGTIRGDFAVDVGRNVCHGSDSVDSAKREIAFWFKPEELVNWTSHSVKQVYE 151
               SCOP domains d3prvf_ F: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee.....................hhhhhh....eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhh...........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3prv F   2 TSERTFIAVKPDGVQRCLVGEIIQRFEKKGYKLVALKMLQPSAEQAQQHYIDLASKPFYKDLVAYFSSGPIVGMVWEGKGVVKGGRVLLGATNPADSLPGTIRGDFAVDVGRNVCHGSDSVDSAKREIAFWFKPEELVNWTSHSVKQVYE 151
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

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/Biological 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: automated matches (17)

Protein domain: automated matches (17)

Trypanosoma cruzi [TaxId: 5693] (1)

1a	d3prva_	A:
1b	d3prvb_	B:
1c	d3prvc_	C:
1d	d3prvd_	D:
1e	d3prve_	E:
1f	d3prvf_	F:

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D,E,F (Q4E256_TRYCC | Q4E256)

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: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: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
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3prv)

	Sites
(no "Sites" information available for 3prv)

	Cis Peptide Bonds
		Ala B:55 - Ser B:56	[ RasMol ]
		Asp F:53 - Leu F:54	[ RasMol ]
		Gln F:48 - Gln F:49	[ RasMol ]
		Gln F:49 - His F:50	[ RasMol ]
		Gly D:81 - Val D:82	[ RasMol ]
		Leu A:54 - Ala A:55	[ RasMol ]
		Leu D:54 - Ala D:55	[ RasMol ]
		Lys B:57 - Pro B:58	[ RasMol ]
		Phe A:59 - Tyr A:60	[ RasMol ]
		Ser F:56 - Lys F:57	[ RasMol ]
		Thr C:2 - Ser C:3	[ RasMol ]
		Thr E:2 - Ser E:3	[ RasMol ]
		Thr F:2 - Ser F:3	[ RasMol ]

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	3prv
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
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	Q4E256_TRYCC \| Q4E256
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	2.7.4.6
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		Interatomic Contacts of Structural Units	:	CSU
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	Q4E256_TRYCC \| Q4E256
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(no "Entries Sharing at Least One Protein Chain" available for 3PRV)

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (13, 13)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 6)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

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