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(-) Description

Title :  STRUCTURE OF NDPK H122G AND TENOFOVIR-DIPHOSPHATE
 
Authors :  S. Morera, Y. X. Chen
Date :  16 Dec 08  (Deposition) - 29 Sep 09  (Release) - 18 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  An Hexamer Structure, Atp-Binding, Kinase, Magnesium, Metal-Binding, Nucleotide Metabolism, Nucleotide-Binding, Phosphoprotein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Koch, Y. X. Chen, J. Y. Feng, K. Borroto-Esoda, D. Deville-Bonne, S. Gallois-Montbrun, J. Janin, S. Morera
Nucleoside Diphosphate Kinase And The Activation Of Antiviral Phosphonate Analogs Of Nucleotides: Binding Mode And Phosphorylation Of Tenofovir Derivatives
Nucleosides Nucleotides V. 28 776 2009 Nucleic Acids
PubMed-ID: 20183617  |  Reference-DOI: 10.1080/15257770903155899

(-) Compounds

Molecule 1 - NUCLEOSIDE DIPHOSPHATE KINASE, CYTOSOLIC
    Chains: A, B, C, D, E, F
    EC Number: 2.7.4.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: SLIME MOLD
    Organism Scientific: DICTYOSTELIUM DISCOIDEUM
    Organism Taxid: 44689
    Synonym: NDP KINASE, NDK

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 19)

Asymmetric/Biological Unit (5, 19)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2GOL2Ligand/IonGLYCEROL
3MG6Ligand/IonMAGNESIUM ION
4TNM5Ligand/Ion[(2R)-1-(6-AMINOPURIN-9-YL)PROPAN-2-YL]OXYMETHYL-PHOSPHONOOXY-PHOSPHINIC ACID
5TNV1Ligand/Ion[2-(6-AMINO-9H-PURIN-9-YL)-1-METHYLETHOXY]METHYL-TRIPHOSPHATE

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:16 , PHE A:64 , LEU A:68 , ARG A:92 , THR A:98 , ARG A:109 , VAL A:116 , ASN A:119 , MG A:156 , HOH A:1016 , HOH A:1017 , HOH A:1019 , HOH A:1022 , HOH A:1282 , HOH A:1335 , HOH A:1428 , HOH A:1626 , HOH A:1627 , HOH A:1861 , HOH B:1863BINDING SITE FOR RESIDUE TNM A 160
02AC2SOFTWARETNM A:160 , HOH A:1016 , HOH A:1019 , HOH A:1020 , HOH A:1335BINDING SITE FOR RESIDUE MG A 156
03AC3SOFTWAREGLU A:146 , LYS A:148 , HOH A:1928 , SER D:74 , GLY D:75 , PRO D:76BINDING SITE FOR RESIDUE EDO A 157
04AC4SOFTWARELYS B:16 , HIS B:59 , PHE B:64 , LEU B:68 , ARG B:92 , THR B:98 , ARG B:109 , VAL B:116 , GLY B:117 , ASN B:119 , MG B:156 , HOH B:1011 , HOH B:1012 , HOH B:1554 , HOH B:1597 , HOH B:1814 , HOH B:1842 , HOH B:1843 , HOH B:1845 , HOH B:2040BINDING SITE FOR RESIDUE TNM B 160
05AC5SOFTWARETNM B:160 , HOH B:1554 , HOH B:1597 , HOH B:1814 , HOH B:2040BINDING SITE FOR RESIDUE MG B 156
06AC6SOFTWAREVAL B:38 , LYS B:148 , HOH B:1405 , HOH B:1505 , HOH B:1694 , HOH B:1794 , ALA E:21 , HOH E:1641BINDING SITE FOR RESIDUE EDO B 157
07AC7SOFTWARELYS C:16 , TYR C:56 , HIS C:59 , PHE C:64 , LEU C:68 , ARG C:92 , ARG C:109 , VAL C:116 , ASN C:119 , MG C:156 , HOH C:1013 , HOH C:1014 , HOH C:1317 , HOH C:1848 , HOH C:1849 , HOH C:1850 , HOH C:1851 , HOH C:2043 , HOH C:2158BINDING SITE FOR RESIDUE TNM C 160
08AC8SOFTWARETNM C:160 , HOH C:1014 , HOH C:1849 , HOH C:1850 , HOH C:1851BINDING SITE FOR RESIDUE MG C 156
09AC9SOFTWAREARG C:92 , GLY C:96 , VAL C:97 , THR C:98 , HOH C:1623 , HOH C:1856 , HOH C:1962BINDING SITE FOR RESIDUE GOL C 157
10BC1SOFTWARELYS D:16 , TYR D:56 , GLU D:58 , HIS D:59 , PHE D:64 , ARG D:92 , ARG D:109 , VAL D:116 , GLY D:117 , ASN D:119 , MG D:156 , HOH D:1001 , HOH D:1005 , HOH D:1327 , HOH D:1831 , HOH D:1834 , HOH D:2154BINDING SITE FOR RESIDUE TNV D 160
11BC2SOFTWARETNV D:160 , HOH D:1001 , HOH D:1831 , HOH D:1834BINDING SITE FOR RESIDUE MG D 156
12BC3SOFTWAREASN D:99 , HOH D:2257 , HOH F:1599BINDING SITE FOR RESIDUE GOL D 157
13BC4SOFTWAREVAL D:38 , LYS D:148 , PRO D:149 , ASN D:150 , TYR D:154 , HOH D:1572 , HOH D:1961 , HOH D:2276BINDING SITE FOR RESIDUE EDO D 158
14BC5SOFTWAREHOH D:1868 , LYS E:16 , HIS E:59 , PHE E:64 , LEU E:68 , ARG E:92 , THR E:98 , ARG E:109 , VAL E:116 , ASN E:119 , MG E:156 , HOH E:1024 , HOH E:1025 , HOH E:1026 , HOH E:1028 , HOH E:1029 , HOH E:1032 , HOH E:1372 , HOH E:1581 , HOH E:1590 , HOH E:1864BINDING SITE FOR RESIDUE TNM E 160
15BC6SOFTWARETNM E:160 , HOH E:1024 , HOH E:1025 , HOH E:1026 , HOH E:1029BINDING SITE FOR RESIDUE MG E 156
16BC7SOFTWAREGLU E:155 , HOH E:2090 , LYS F:16 , PHE F:64 , LEU F:68 , ARG F:92 , THR F:98 , ARG F:109 , VAL F:116 , ASN F:119 , MG F:156 , HOH F:1036 , HOH F:1038 , HOH F:1043 , HOH F:1045 , HOH F:1046 , HOH F:1049 , HOH F:1050 , HOH F:1106 , HOH F:1869BINDING SITE FOR RESIDUE TNM F 160
17BC8SOFTWARETNM F:160 , HOH F:1043 , HOH F:1044 , HOH F:1045 , HOH F:1046BINDING SITE FOR RESIDUE MG F 156
18BC9SOFTWAREHOH E:1307 , GLY F:67 , SER F:70 , PHE F:71BINDING SITE FOR RESIDUE EDO F 157
19CC1SOFTWAREVAL F:6 , ASN F:7BINDING SITE FOR RESIDUE EDO F 158

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 6)

Asymmetric/Biological Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NDP_KINASESPS00469 Nucleoside diphosphate kinases active site.NDKC_DICDI119-127
 
 
 
 
 		  6A:119-127
B:119-127
C:119-127
D:119-127
E:119-127
F:119-127

(-) Exons   (0, 0)

(no "Exon" information available for 3FKB)

(-) Sequences/Alignments

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 NDKC_DICDI | P22887 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:150
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155
           NDKC_DICDI     6 VNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIHGSDSVESANREIALWFKPEELLTEVKPNPNLYE 155
               SCOP domains d3fkba_ 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............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------NDP_KINAS---------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3fkb A   6 VNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIGGSDSVESANREIALWFKPEELLTEVKPNPNLYE 155
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155


Chain B from PDB  Type:PROTEIN  Length:150
 aligned with NDKC_DICDI | P22887 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:150
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155
           NDKC_DICDI     6 VNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIHGSDSVESANREIALWFKPEELLTEVKPNPNLYE 155
               SCOP domains d3fkbb_ 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............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------NDP_KINAS---------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3fkb B   6 VNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIGGSDSVESANREIALWFKPEELLTEVKPNPNLYE 155
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155


Chain C from PDB  Type:PROTEIN  Length:150
 aligned with NDKC_DICDI | P22887 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:150
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155
           NDKC_DICDI     6 VNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIHGSDSVESANREIALWFKPEELLTEVKPNPNLYE 155
               SCOP domains d3fkbc_ C: 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............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------NDP_KINAS---------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3fkb C   6 VNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIGGSDSVESANREIALWFKPEELLTEVKPNPNLYE 155
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155


Chain D from PDB  Type:PROTEIN  Length:149
 aligned with NDKC_DICDI | P22887 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:149
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146         
           NDKC_DICDI     7 NKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIHGSDSVESANREIALWFKPEELLTEVKPNPNLYE 155
               SCOP domains d3fkbd_ D: 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............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------NDP_KINAS---------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fkb D   7 NKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIGGSDSVESANREIALWFKPEELLTEVKPNPNLYE 155
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146         


Chain E from PDB  Type:PROTEIN  Length:149
 aligned with NDKC_DICDI | P22887 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:149
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146         
           NDKC_DICDI     7 NKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIHGSDSVESANREIALWFKPEELLTEVKPNPNLYE 155
               SCOP domains d3fkbe_ E: 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............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------NDP_KINAS---------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fkb E   7 NKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIGGSDSVESANREIALWFKPEELLTEVKPNPNLYE 155
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146         


Chain F from PDB  Type:PROTEIN  Length:150
 aligned with NDKC_DICDI | P22887 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:150
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155
           NDKC_DICDI     6 VNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIHGSDSVESANREIALWFKPEELLTEVKPNPNLYE 155
               SCOP domains d3fkbf_ F: 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............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------NDP_KINAS---------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3fkb F   6 VNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIGGSDSVESANREIALWFKPEELLTEVKPNPNLYE 155
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155
   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, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (NDKC_DICDI | P22887)
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:0007186    G-protein coupled receptor signaling pathway    A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
    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:0030036    actin cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0016049    cell growth    The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
    GO:0006186    dGDP phosphorylation    The process of introducing a phosphate group into dGDP, deoxyguanosine diphosphate, to produce dGTP.
    GO:0006187    dGTP biosynthetic process from dGDP    The chemical reactions and pathways resulting in the formation of dGTP, deoxyguanosine triphosphate (2'-deoxyguanosine 5'-triphosphate) from other compounds, including gGDP, deoxyguanosine diphosphate.
    GO:0044351    macropinocytosis    An endocytosis process that results in the uptake of liquid material by cells from their external environment by the 'ruffling' of the cell membrane to form heterogeneously sized intracellular vesicles called macropinosomes, which can be up to 5 micrometers in size.
    GO:0045920    negative regulation of exocytosis    Any process that stops, prevents, or reduces the frequency, rate or extent of exocytosis.
    GO:0050765    negative regulation of phagocytosis    Any process that stops, prevents, or reduces the frequency, rate or extent of phagocytosis.
    GO:0048550    negative regulation of pinocytosis    Any process that stops, prevents, or reduces the frequency, rate or extent of pinocytosis. Pinocytosis is the process in which cells take in liquid material from their external environment; literally 'cell drinking'. Liquid is enclosed in vesicles, formed by invagination of the plasma membrane. These vesicles then move into the cell and pass their contents to endosomes.
    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: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:0009617    response to bacterium    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a bacterium.
    GO:0006414    translational elongation    The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
cellular component
    GO:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0045335    phagocytic vesicle    A membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0005840    ribosome    An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
    GO:0030141    secretory granule    A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.

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 Related Entries

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        NDKC_DICDI | P22887: 1b4s 1b99 1bux 1f3f 1f6t 1hhq 1hiy 1hlw 1kdn 1leo 1lwx 1mn7 1mn9 1ncl 1ndc 1ndk 1ndp 1npk 1nsp 1pae 1s5z 2bef 4c6a 4cp5

(-) Related Entries Specified in the PDB File

1b4s 1f3f 2bef