4DZ6 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   TRANSITION STATE MIMIC OF NUCLEOSIDE-DIPHOSPHATE KINASE FROM BORRELIA BURGDORFERI WITH BOUND VANADATE AND ADP

Authors :   Seattle Structural Genomics Center For Infectious Disease (S

Date :   29 Feb 12 (Deposition) - 14 Mar 12 (Release) - 14 Mar 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Ssgcid, Niaid, Nucleoside Diphosphate Kinase, Kinase, Vanadate, Transition State Mimic, Transition State Analog, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Seattle Structural Genomics Center For Infectious Disease (Ssgcid), D. R. Davies, A. Gardberg, B. Staker, L. Stewart
Transition State Mimic Of Nucleoside-Diphosphate Kinase Fro Borrelia Burgdorferi With Bound Vanadate And Adp
To Be Published
PubMed: search

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	:	AVA0421
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	NUCLEOSIDE-DIPHOSPHATE KINASE
	Gene	:	NDK, BB_0463
	Organism Common	:	LYME DISEASE SPIROCHETE
	Organism Scientific	:	BORRELIA BURGDORFERI
	Organism Taxid	:	139
	Synonym	:	NDK, NDP KINASE, NUCLEOSIDE-2-P KINASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 11)

No.	Name	Count	Type	Full Name
1	ADP	3	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	VN4	3	Ligand/Ion	OXIDO(DIOXO)VANADIUM
4	VO4	3	Ligand/Ion	VANADATE ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:13 , ARG A:61 , HIS A:62 , LEU A:70 , ARG A:94 , THR A:100 , ARG A:111 , PHE A:119 , SER A:122 , ILE A:129 , ASN A:131 , VN4 A:1002 , HOH A:1107	BINDING SITE FOR RESIDUE ADP A 1001
02	AC2	SOFTWARE	LYS A:13 , TYR A:53 , ARG A:94 , ARG A:111 , HIS A:134 , ALA A:135 , ADP A:1001	BINDING SITE FOR RESIDUE VN4 A 1002
03	AC3	SOFTWARE	LYS A:40 , ILE A:148 , TRP A:149	BINDING SITE FOR RESIDUE EDO A 1003
04	AC4	SOFTWARE	LYS B:13 , TYR B:53 , ARG B:94 , ARG B:111 , HIS B:134 , ALA B:135	BINDING SITE FOR RESIDUE VO4 B 201
05	AC5	SOFTWARE	ASP A:162 , HOH A:1114 , ARG B:19 , ARG C:19 , ASP E:162 , HOH E:328	BINDING SITE FOR RESIDUE EDO B 202
06	AC6	SOFTWARE	LYS C:13 , ARG C:61 , HIS C:62 , LEU C:70 , ARG C:94 , THR C:100 , ARG C:111 , PHE C:119 , SER C:122 , SER C:128 , ILE C:129 , ASN C:131 , VN4 C:1002	BINDING SITE FOR RESIDUE ADP C 1001
07	AC7	SOFTWARE	LYS C:13 , TYR C:53 , ARG C:94 , ARG C:111 , HIS C:134 , ALA C:135 , ADP C:1001	BINDING SITE FOR RESIDUE VN4 C 1002
08	AC8	SOFTWARE	LYS D:13 , ARG D:61 , HIS D:62 , LEU D:70 , ARG D:94 , THR D:100 , ARG D:111 , PHE D:119 , SER D:122 , ASN D:123 , SER D:128 , ILE D:129 , ASN D:131 , VN4 D:1002	BINDING SITE FOR RESIDUE ADP D 1001
09	AC9	SOFTWARE	LYS D:13 , TYR D:53 , ARG D:111 , HIS D:134 , ALA D:135 , ADP D:1001	BINDING SITE FOR RESIDUE VN4 D 1002
10	BC1	SOFTWARE	LYS E:13 , TYR E:53 , ARG E:94 , ARG E:111 , HIS E:134 , ALA E:135	BINDING SITE FOR RESIDUE VO4 E 201
11	BC2	SOFTWARE	LYS F:13 , TYR F:53 , ARG F:94 , ARG F:111 , HIS F:134 , ALA F:135	BINDING SITE FOR RESIDUE VO4 F 201

Asymmetric/Biological Unit

No.	Residues
1	A:164	-	A:169
2	B:164	-	B:169
3	C:164	-	C:169
4	D:164	-	D:169
5	E:164	-	E:169
6	F:164	-	F:169

(no "Cis Peptide Bond" information available for 4DZ6)

(no "SAP(SNP)/Variant" information available for 4DZ6)

(no "PROSITE Motif" information available for 4DZ6)

(no "Exon" information available for 4DZ6)

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:168
 aligned with NDK_BORBU | O51419 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:168
                             1                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159        
            NDK_BORBU     - -MLLQKTLCIVKPDGVRRGLIGDVVSRFERVGLKMVAAKMLIVDESLAKKHYLYDDIVFRHSEAVWNSLIKFISNSPVFTFVVEGVESIEVVRKLCGATEPKLAIPGTIRGDFSYHSFKYSNEKGFSIYNVIHASANEADAMREIPIWFKDNEILNYKRDDECEHYYC 167
               SCOP domains d4dz6a_ A: automated matches                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeehhhhhhhhhhh..hhhhh...hhhhhhh..hhhhhhhhh......eee..hhhhhhhhhhhhhhhhhh......hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dz6 A   2 SMLLQKTLCIVKPDGVRRGLIGDVVSRFERVGLKMVAAKMLIVDESLAKKHYLYDDIVFRHSEAVWNSLIKFISNSPVFTFVVEGVESIEVVRKLCGATEPKLAIPGTIRGDFSYHSFKYSNEKGFSIYNVIHASANEADAMREIPIWFKDNEILNYKRDDECEHYYC 169
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain B from PDB  Type:PROTEIN  Length:168
 aligned with NDK_BORBU | O51419 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:168
                             1                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159        
            NDK_BORBU     - -MLLQKTLCIVKPDGVRRGLIGDVVSRFERVGLKMVAAKMLIVDESLAKKHYLYDDIVFRHSEAVWNSLIKFISNSPVFTFVVEGVESIEVVRKLCGATEPKLAIPGTIRGDFSYHSFKYSNEKGFSIYNVIHASANEADAMREIPIWFKDNEILNYKRDDECEHYYC 167
               SCOP domains d4dz6b_ B: automated matches                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhh..........hhhhhhh..hhhhhhhhh......eee..hhhhhhhhhhhhhhhhhh......hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dz6 B   2 SMLLQKTLCIVKPDGVRRGLIGDVVSRFERVGLKMVAAKMLIVDESLAKKHYLYDDIVFRHSEAVWNSLIKFISNSPVFTFVVEGVESIEVVRKLCGATEPKLAIPGTIRGDFSYHSFKYSNEKGFSIYNVIHASANEADAMREIPIWFKDNEILNYKRDDECEHYYC 169
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain C from PDB  Type:PROTEIN  Length:168
 aligned with NDK_BORBU | O51419 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:168
                             1                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159        
            NDK_BORBU     - -MLLQKTLCIVKPDGVRRGLIGDVVSRFERVGLKMVAAKMLIVDESLAKKHYLYDDIVFRHSEAVWNSLIKFISNSPVFTFVVEGVESIEVVRKLCGATEPKLAIPGTIRGDFSYHSFKYSNEKGFSIYNVIHASANEADAMREIPIWFKDNEILNYKRDDECEHYYC 167
               SCOP domains d4dz6c_ C: automated matches                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhh..........hhhhhhh..hhhhhhhhh......eee..hhhhhhhhhhhhhhhhhh......hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dz6 C   2 SMLLQKTLCIVKPDGVRRGLIGDVVSRFERVGLKMVAAKMLIVDESLAKKHYLYDDIVFRHSEAVWNSLIKFISNSPVFTFVVEGVESIEVVRKLCGATEPKLAIPGTIRGDFSYHSFKYSNEKGFSIYNVIHASANEADAMREIPIWFKDNEILNYKRDDECEHYYC 169
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain D from PDB  Type:PROTEIN  Length:168
 aligned with NDK_BORBU | O51419 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:168
                             1                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159        
            NDK_BORBU     - -MLLQKTLCIVKPDGVRRGLIGDVVSRFERVGLKMVAAKMLIVDESLAKKHYLYDDIVFRHSEAVWNSLIKFISNSPVFTFVVEGVESIEVVRKLCGATEPKLAIPGTIRGDFSYHSFKYSNEKGFSIYNVIHASANEADAMREIPIWFKDNEILNYKRDDECEHYYC 167
               SCOP domains d4dz6d_ D: automated matches                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeehhhhhhhhhhh..........hhhhhhh..hhhhhhhhh......eee..hhhhhhhhhhhhhhhhhh......hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dz6 D   2 SMLLQKTLCIVKPDGVRRGLIGDVVSRFERVGLKMVAAKMLIVDESLAKKHYLYDDIVFRHSEAVWNSLIKFISNSPVFTFVVEGVESIEVVRKLCGATEPKLAIPGTIRGDFSYHSFKYSNEKGFSIYNVIHASANEADAMREIPIWFKDNEILNYKRDDECEHYYC 169
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain E from PDB  Type:PROTEIN  Length:168
 aligned with NDK_BORBU | O51419 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:168
                             1                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159        
            NDK_BORBU     - -MLLQKTLCIVKPDGVRRGLIGDVVSRFERVGLKMVAAKMLIVDESLAKKHYLYDDIVFRHSEAVWNSLIKFISNSPVFTFVVEGVESIEVVRKLCGATEPKLAIPGTIRGDFSYHSFKYSNEKGFSIYNVIHASANEADAMREIPIWFKDNEILNYKRDDECEHYYC 167
               SCOP domains d4dz6e_ E: automated matches                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhh..hhhhh...hhhhhhh..hhhhhhhhh......eee..hhhhhhhhhhhhhhhhhh......hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dz6 E   2 SMLLQKTLCIVKPDGVRRGLIGDVVSRFERVGLKMVAAKMLIVDESLAKKHYLYDDIVFRHSEAVWNSLIKFISNSPVFTFVVEGVESIEVVRKLCGATEPKLAIPGTIRGDFSYHSFKYSNEKGFSIYNVIHASANEADAMREIPIWFKDNEILNYKRDDECEHYYC 169
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain F from PDB  Type:PROTEIN  Length:168
 aligned with NDK_BORBU | O51419 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:168
                             1                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159        
            NDK_BORBU     - -MLLQKTLCIVKPDGVRRGLIGDVVSRFERVGLKMVAAKMLIVDESLAKKHYLYDDIVFRHSEAVWNSLIKFISNSPVFTFVVEGVESIEVVRKLCGATEPKLAIPGTIRGDFSYHSFKYSNEKGFSIYNVIHASANEADAMREIPIWFKDNEILNYKRDDECEHYYC 167
               SCOP domains d4dz6f_ F: automated matches                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..eeeeeeeeeehhhhhhhhhhh..........hhhhhhh..hhhhhhhhh......eee..hhhhhhhhhhhhhhhhhh......hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dz6 F   2 SMLLQKTLCIVKPDGVRRGLIGDVVSRFERVGLKMVAAKMLIVDESLAKKHYLYDDIVFRHSEAVWNSLIKFISNSPVFTFVVEGVESIEVVRKLCGATEPKLAIPGTIRGDFSYHSFKYSNEKGFSIYNVIHASANEADAMREIPIWFKDNEILNYKRDDECEHYYC 169
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

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)

Lyme disease spirochete (Borrelia burgdorferi) [TaxId: 139] (2)

1a	d4dz6a_	A:
1b	d4dz6b_	B:
1c	d4dz6c_	C:
1d	d4dz6d_	D:
1e	d4dz6e_	E:
1f	d4dz6f_	F:

(no "CATH Domain" information available for 4DZ6)

(no "Pfam Domain" information available for 4DZ6)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D,E,F (NDK_BORBU | O51419)

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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4dz6)

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	4dz6
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	NDK_BORBU \| O51419	:	4di6

4di6	UNLIGANDED STRUCTURE RELATED ID: BOBUA.00664.A RELATED DB: TARGETTRACK

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 11)

Sites (11, 11)

SS Bonds (6, 6)

Cis Peptide Bonds (0, 0)

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 (13, 13)

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