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(-) Description

Title :  STRUCTURE OF HUMAN NUCLEOSIDE-DIPHOSPHATE KINASE 3
 
Authors :  J. Choe, S. Dimov, C. Arrowsmith, A. Edwards, M. Sundstrom, A. Bochkare Structural Genomics Consortium (Sgc)
Date :  23 May 05  (Deposition) - 07 Jun 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,D
Biol. Unit 1:  A,B,D  (2x)
Keywords :  Nucleotide Metabolism, Apoptosis, Kinase, Transferase, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Dimov, J. Choe, C. Arrowsmith, A. Edwards, M. Sundstrom, A. Bochkarev, H. Park
Structure Of Human Nucleoside-Diphosphate Kinase 3
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NUCLEOSIDE DIPHOSPHATE KINASE 3
    ChainsA, B, D
    EC Number2.7.4.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneNME3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNDK 3, NDP KINASE 3, NUCLEOSIDE DIPHOSPHATE KINASE C, NDPKC, NM23-H3, DR-NM23

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABD
Biological Unit 1 (2x)ABD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1ADP3Ligand/IonADENOSINE-5'-DIPHOSPHATE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1ADP6Ligand/IonADENOSINE-5'-DIPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:29 , PHE A:77 , LEU A:81 , ARG A:105 , THR A:111 , ARG A:122 , VAL A:129 , ASN A:132BINDING SITE FOR RESIDUE ADP A 201
2AC2SOFTWAREGLU A:169 , LYS B:29 , TYR B:69 , LEU B:72 , PHE B:77 , LEU B:81 , ARG B:105 , THR B:111 , VAL B:129 , GLY B:130 , ASN B:132 , HOH B:301 , LYS D:83BINDING SITE FOR RESIDUE ADP B 202
3AC3SOFTWARELYS D:29 , TYR D:69 , LEU D:72 , PHE D:77 , LEU D:81 , ARG D:105 , THR D:111 , ARG D:122 , VAL D:129 , ASN D:132 , HOH D:307 , HOH D:321BINDING SITE FOR RESIDUE ADP D 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZS6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ZS6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZS6)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NDP_KINASESPS00469 Nucleoside diphosphate kinases active site.NDK3_HUMAN132-140
 
 
  3A:132-140
B:132-140
D:132-140
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NDP_KINASESPS00469 Nucleoside diphosphate kinases active site.NDK3_HUMAN132-140
 
 
  6A:132-140
B:132-140
D:132-140

(-) Exons   (4, 12)

Asymmetric Unit (4, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002193021ENSE00001273366chr16:1821710-1821490221NDK3_HUMAN1-16160--
1.2ENST000002193022ENSE00000683466chr16:1821411-1821281131NDK3_HUMAN16-59443A:18-59
B:18-59
D:18-59
42
42
42
1.3ENST000002193023ENSE00000683469chr16:1821172-1821071102NDK3_HUMAN60-93343A:60-93
B:60-93
D:60-93
34
34
34
1.4ENST000002193024ENSE00000683471chr16:1820994-1820882113NDK3_HUMAN94-131383A:94-131
B:94-131
D:94-131
38
38
38
1.5ENST000002193025ENSE00000892274chr16:1820767-1820321447NDK3_HUMAN131-169393A:131-169
B:131-169
D:131-169
39
39
39

(-) Sequences/Alignments

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:152
 aligned with NDK3_HUMAN | Q13232 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:152
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167  
           NDK3_HUMAN    18 TGAHERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLVQASEELLREHYAELRERPFYGRLVKYMASGPVVAMVWQGLDVVRTSRALIGATNPADAPPGTIRGDFCIEVGKNLIHGSDSVESARREIALWFRADELLCWEDSAGHWLYE 169
               SCOP domains d1zs6a1 A:18-169 Nucleoside diphosphate kinase, NDK                                                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh.eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------NDP_KINAS----------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:18-59 UniProt: 16-59     Exon 1.3  PDB: A:60-93            Exon 1.4  PDB: A:94-131               -------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------Exon 1.5  PDB: A:131-169                Transcript 1 (2)
                 1zs6 A  18 TGAHERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLVQASEELLREHYAELRERPFYGRLVKYMASGPVVAMVWQGLDVVRTSRALIGATNPADAPPGTIRGDFCIEVGKNLIHGSDSVESARREIALWFRADELLCWEDSAGHWLYE 169
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167  

Chain B from PDB  Type:PROTEIN  Length:152
 aligned with NDK3_HUMAN | Q13232 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:152
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167  
           NDK3_HUMAN    18 TGAHERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLVQASEELLREHYAELRERPFYGRLVKYMASGPVVAMVWQGLDVVRTSRALIGATNPADAPPGTIRGDFCIEVGKNLIHGSDSVESARREIALWFRADELLCWEDSAGHWLYE 169
               SCOP domains d1zs6b_ B: Nucleoside diphosphate kinase, NDK                                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh.eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------NDP_KINAS----------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:18-59 UniProt: 16-59     Exon 1.3  PDB: B:60-93            Exon 1.4  PDB: B:94-131               -------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------Exon 1.5  PDB: B:131-169                Transcript 1 (2)
                 1zs6 B  18 TGAHERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLVQASEELLREHYAELRERPFYGRLVKYMASGPVVAMVWQGLDVVRTSRALIGATNPADAPPGTIRGDFCIEVGKNLIHGSDSVESARREIALWFRADELLCWEDSAGHWLYE 169
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167  

Chain D from PDB  Type:PROTEIN  Length:152
 aligned with NDK3_HUMAN | Q13232 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:152
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167  
           NDK3_HUMAN    18 TGAHERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLVQASEELLREHYAELRERPFYGRLVKYMASGPVVAMVWQGLDVVRTSRALIGATNPADAPPGTIRGDFCIEVGKNLIHGSDSVESARREIALWFRADELLCWEDSAGHWLYE 169
               SCOP domains d1zs6d_ D: Nucleoside diphosphate kinase, NDK                                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----NDK-1zs6D01 D:22-156                                                                                                                   ------------- Pfam domains (1)
           Pfam domains (2) ----NDK-1zs6D02 D:22-156                                                                                                                   ------------- Pfam domains (2)
           Pfam domains (3) ----NDK-1zs6D03 D:22-156                                                                                                                   ------------- Pfam domains (3)
         Sec.struct. author hhhh.eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..........hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------NDP_KINAS----------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: D:18-59 UniProt: 16-59     Exon 1.3  PDB: D:60-93            Exon 1.4  PDB: D:94-131               -------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------Exon 1.5  PDB: D:131-169                Transcript 1 (2)
                 1zs6 D  18 TGAHERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLVQASEELLREHYAELRERPFYGRLVKYMASGPVVAMVWQGLDVVRTSRALIGATNPADAPPGTIRGDFCIEVGKNLIHGSDSVESARREIALWFRADELLCWEDSAGHWLYE 169
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167  

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 3)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1ZS6)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Family: NDK (40)
1aNDK-1zs6D01D:22-156
1bNDK-1zs6D02D:22-156
1cNDK-1zs6D03D:22-156

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B,D   (NDK3_HUMAN | Q13232)
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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    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: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.
    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.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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