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Title :   STRUCTURE OF LEISHMANIA NUCLEOSIDE DIPHOSPHATE KINASE B WITH ORDERED NUCLEOTIDE-BINDING LOOP

Authors :   D. M. Trindade, T. A. C. B Sousa, C. C. C. Tonoli, C. R. Santos, R. K. Arni, A. H. C. Oliveira, M. T. Murakami

Date :   13 Jun 10 (Deposition) - 27 Apr 11 (Release) - 09 Oct 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Lmndkb, Phosphate Ion, Ordered Nucleotide-Binding Loop, Transferase (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
	EC Number	:	2.7.4.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	L1648.07, LMJF32.2950, NDKB
	Organism Scientific	:	LEISHMANIA MAJOR
	Organism Taxid	:	5664

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	DTT	1	Ligand/Ion	2,3-DIHYDROXY-1,4-DITHIOBUTANE
2	PO4	3	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	DTT	2	Ligand/Ion	2,3-DIHYDROXY-1,4-DITHIOBUTANE
2	PO4	6	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:11 , TYR A:51 , ARG A:104 , ASN A:114 , CYS A:116 , HIS A:117 , PO4 A:153 , HOH A:248 , HOH A:288	BINDING SITE FOR RESIDUE PO4 A 152
2	AC2	SOFTWARE	ARG A:87 , THR A:93 , ARG A:104 , HIS A:117 , GLY A:118 , PO4 A:152 , HOH A:220	BINDING SITE FOR RESIDUE PO4 A 153
3	AC3	SOFTWARE	HOH A:276 , LYS B:11 , HIS B:50 , ARG B:87 , THR B:93 , ASN B:114 , HIS B:117 , HOH B:289	BINDING SITE FOR RESIDUE DTT B 152
4	AC4	SOFTWARE	LYS C:11 , THR C:93 , ASN C:114 , CYS C:116 , HIS C:117 , HOH C:353 , HOH C:361	BINDING SITE FOR RESIDUE PO4 C 152

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

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

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

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

(no "Exon" information available for 3NGS)

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:151
 aligned with Q9U1E1_LEIMA | Q9U1E1 from UniProtKB/TrEMBL  Length:151

    Alignment length:151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 
         Q9U1E1_LEIMA     1 MSSERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
               SCOP domains d3ngsa_ A: automated matches                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ngs A   1 MSSERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:150
 aligned with Q9U1E1_LEIMA | Q9U1E1 from UniProtKB/TrEMBL  Length:151

    Alignment length:150
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151
         Q9U1E1_LEIMA     2 SSERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
               SCOP domains d3ngsb_ B: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ngs B   2 SSERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain C from PDB  Type:PROTEIN  Length:151
 aligned with Q9U1E1_LEIMA | Q9U1E1 from UniProtKB/TrEMBL  Length:151

    Alignment length:151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 
         Q9U1E1_LEIMA     1 MSSERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
               SCOP domains d3ngsc_ C: automated matches                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---NDK-3ngsC01 C:4-138                                                                                                                    ------------- Pfam domains (1)
           Pfam domains (2) ---NDK-3ngsC02 C:4-138                                                                                                                    ------------- Pfam domains (2)
           Pfam domains (3) ---NDK-3ngsC03 C:4-138                                                                                                                    ------------- Pfam domains (3)
         Sec.struct. author ....eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ngs C   1 MSSERTFIAVKPDGVQRGLVGEIIARFERKGYKLVALKILQPTTEQAQGHYKDLCSKPFFPALVKYFSSGPIVCMVWEGKNVVKSGRVLLGATNPADSQPGTIRGDFAVDVGRNVCHGSDSVESAEREIAFWFKADEIASWTSHSVSQIYE 151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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)

Leishmania major [TaxId: 5664] (4)

1a	d3ngsa_	A:
1b	d3ngsb_	B:
1c	d3ngsc_	C:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: NDK] (40)

Family: NDK (40)

Leishmania major (4)

1a	NDK-3ngsC01	C:4-138
1b	NDK-3ngsC02	C:4-138
1c	NDK-3ngsC03	C:4-138

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (Q9U1E1_LEIMA | Q9U1E1)

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:0009142	nucleoside triphosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar.
	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:0006163	purine nucleotide metabolic process	The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	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:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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Biological Unit
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	Q9U1E1_LEIMA \| Q9U1E1	:	3ngr 3ngt 3ngu 5c7p 5caa 5cab

3ngr	THE SAME PROTEIN WITH UNORDERED NUCLEOTIDE-BINDING LOOP
3ngt	THE SAME PROTEIN COMPLEXED WITH AMP.
3ngu	THE SAME PROTEIN COMPLEXED WITH ADP.

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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