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 R1A_IBVBC               Reviewed;        3951 AA.
P0C6V4; Q91QT2;
10-JUN-2008, integrated into UniProtKB/Swiss-Prot.
10-JUN-2008, sequence version 1.
25-OCT-2017, entry version 51.
RecName: Full=Replicase polyprotein 1a;
Short=pp1a;
AltName: Full=ORF1a polyprotein;
Contains:
RecName: Full=Non-structural protein 2;
Short=nsp2;
AltName: Full=p87;
Contains:
RecName: Full=Non-structural protein 3;
Short=nsp3;
EC=3.4.22.-;
AltName: Full=Papain-like proteinase;
Short=PL-PRO;
AltName: Full=p195;
Contains:
RecName: Full=Non-structural protein 4;
Short=nsp4;
AltName: Full=Peptide HD2;
AltName: Full=p41;
Contains:
RecName: Full=3C-like proteinase;
Short=3CL-PRO;
Short=3CLp;
EC=3.4.22.-;
AltName: Full=M-PRO;
AltName: Full=nsp5;
AltName: Full=p33;
Contains:
RecName: Full=Non-structural protein 6;
Short=nsp6;
AltName: Full=p34;
Contains:
RecName: Full=Non-structural protein 7;
Short=nsp7;
AltName: Full=p9;
Contains:
RecName: Full=Non-structural protein 8;
Short=nsp8;
AltName: Full=p24;
Contains:
RecName: Full=Non-structural protein 9;
Short=nsp9;
AltName: Full=p10;
Contains:
RecName: Full=Non-structural protein 10;
Short=nsp10;
AltName: Full=Growth factor-like peptide;
Short=GFL;
AltName: Full=p16;
Contains:
RecName: Full=Non-structural protein 11;
Short=nsp11;
ORFNames=1a;
Avian infectious bronchitis virus (strain Beaudette CK) (IBV).
Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA stage;
Nidovirales; Coronaviridae; Coronavirinae; Gammacoronavirus.
NCBI_TaxID=160235;
NCBI_TaxID=9031; Gallus gallus (Chicken).
[1]
NUCLEOTIDE SEQUENCE [GENOMIC RNA].
Casais R., Thiel V., Siddell S., Cavanagh D., Britton P.;
"Recovery of the avian coronavirus infectious bronchitis virus from
cDNA assembled in vaccinia virus.";
Submitted (MAY-2001) to the EMBL/GenBank/DDBJ databases.
-!- FUNCTION: The papain-like proteinase (PL-PRO) is responsible for
the cleavages located at the N-terminus of replicase polyprotein.
Activity of PL-PRO is dependent on zinc (By similarity).
{ECO:0000250}.
-!- FUNCTION: The main proteinase 3CL-PRO is responsible for the
majority of cleavages as it cleaves the C-terminus of replicase
polyprotein at 11 sites. Recognizes substrates containing the core
sequence [ILMVF]-Q-|-[SGACN]. Inhibited by the substrate-analog
Cbz-Val-Asn-Ser-Thr-Leu-Gln-CMK. {ECO:0000255|PROSITE-
ProRule:PRU00772}.
-!- FUNCTION: The peptide p16 might be involved in the EGF signaling
pathway. {ECO:0000250}.
-!- FUNCTION: Nsp7-nsp8 hexadecamer may possibly confer processivity
to the polymerase, maybe by binding to dsRNA or by producing
primers utilized by the latter. {ECO:0000250}.
-!- FUNCTION: Nsp9 is a ssRNA-binding protein. {ECO:0000250}.
-!- SUBUNIT: 3CL-PRO exists as monomer and homodimer. The three
peptides nsp2, nsp3 and nsp4 may form a complex. Nsp9 is a dimer.
Eight copies of nsp7 and eight copies of nsp8 assemble to form a
heterohexadecamer. Nsp10 forms a dodecamer (By similarity).
{ECO:0000250}.
-!- SUBCELLULAR LOCATION: Non-structural protein 3: Host membrane
{ECO:0000305}; Multi-pass membrane protein {ECO:0000305}.
-!- SUBCELLULAR LOCATION: Non-structural protein 4: Host membrane
{ECO:0000305}; Multi-pass membrane protein {ECO:0000305}.
-!- SUBCELLULAR LOCATION: Non-structural protein 6: Host membrane
{ECO:0000305}; Multi-pass membrane protein {ECO:0000305}.
-!- SUBCELLULAR LOCATION: Non-structural protein 7: Host cytoplasm,
host perinuclear region {ECO:0000250}. Note=nsp7, nsp8, nsp9 and
nsp10 are localized in cytoplasmic foci, largely perinuclear. Late
in infection, they merge into confluent complexes (By similarity).
{ECO:0000250}.
-!- SUBCELLULAR LOCATION: Non-structural protein 8: Host cytoplasm,
host perinuclear region {ECO:0000250}. Note=nsp7, nsp8, nsp9 and
nsp10 are localized in cytoplasmic foci, largely perinuclear. Late
in infection, they merge into confluent complexes (By similarity).
{ECO:0000250}.
-!- SUBCELLULAR LOCATION: Non-structural protein 9: Host cytoplasm,
host perinuclear region {ECO:0000250}. Note=nsp7, nsp8, nsp9 and
nsp10 are localized in cytoplasmic foci, largely perinuclear. Late
in infection, they merge into confluent complexes (By similarity).
{ECO:0000250}.
-!- SUBCELLULAR LOCATION: Non-structural protein 10: Host cytoplasm,
host perinuclear region {ECO:0000250}. Note=nsp7, nsp8, nsp9 and
nsp10 are localized in cytoplasmic foci, largely perinuclear. Late
in infection, they merge into confluent complexes (By similarity).
{ECO:0000250}.
-!- ALTERNATIVE PRODUCTS:
Event=Ribosomal frameshifting; Named isoforms=2;
Name=Replicase polyprotein 1a; Synonyms=pp1a, ORF1a polyprotein;
IsoId=P0C6V4-1; Sequence=Displayed;
Note=Produced by conventional translation.;
Name=Replicase polyprotein 1ab; Synonyms=pp1ab;
IsoId=P0C6Y2-1; Sequence=External;
Note=Produced by -1 ribosomal frameshifting at the 1a-1b genes
boundary.;
-!- DOMAIN: The hydrophobic domains (HD) could mediate the membrane
association of the replication complex and thereby alter the
architecture of the host cell membrane.
-!- PTM: Specific enzymatic cleavages in vivo by its own proteases
yield mature proteins. 3CL-PRO and PL-PRO proteinases are
autocatalytically processed (By similarity). {ECO:0000250}.
-!- SIMILARITY: Belongs to the coronaviruses polyprotein 1ab family.
{ECO:0000305}.
-----------------------------------------------------------------------
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Distributed under the Creative Commons Attribution-NoDerivs License
-----------------------------------------------------------------------
EMBL; AJ311317; CAC39113.1; -; Genomic_RNA.
ProteinModelPortal; P0C6V4; -.
SMR; P0C6V4; -.
Proteomes; UP000114388; Genome.
GO; GO:0033644; C:host cell membrane; IEA:UniProtKB-SubCell.
GO; GO:0044220; C:host cell perinuclear region of cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
GO; GO:0004197; F:cysteine-type endopeptidase activity; IEA:InterPro.
GO; GO:0008242; F:omega peptidase activity; IEA:InterPro.
GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
GO; GO:0003968; F:RNA-directed 5'-3' RNA polymerase activity; IEA:InterPro.
GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
GO; GO:0039520; P:induction by virus of host autophagy; IEA:UniProtKB-KW.
GO; GO:0019079; P:viral genome replication; IEA:InterPro.
GO; GO:0019082; P:viral protein processing; IEA:InterPro.
Gene3D; 2.40.10.250; -; 1.
InterPro; IPR032505; Corona_NSP4_C.
InterPro; IPR002589; Macro_dom.
InterPro; IPR036333; NSP10_sf.
InterPro; IPR014828; NSP7.
InterPro; IPR037204; NSP7_sf.
InterPro; IPR014829; NSP8.
InterPro; IPR037230; NSP8_sf.
InterPro; IPR014822; NSP9.
InterPro; IPR036499; NSP9_sf.
InterPro; IPR008740; Peptidase_C30.
InterPro; IPR013016; Peptidase_C30/C16.
InterPro; IPR009003; Peptidase_S1_PA.
InterPro; IPR018995; RNA_synth_NSP10_coronavirus.
InterPro; IPR014827; Viral_protease.
Pfam; PF16348; Corona_NSP4_C; 1.
Pfam; PF01661; Macro; 1.
Pfam; PF09401; NSP10; 1.
Pfam; PF08716; nsp7; 1.
Pfam; PF08717; nsp8; 1.
Pfam; PF08710; nsp9; 1.
Pfam; PF05409; Peptidase_C30; 1.
Pfam; PF08715; Viral_protease; 1.
SMART; SM00506; A1pp; 1.
SUPFAM; SSF101816; SSF101816; 1.
SUPFAM; SSF140367; SSF140367; 1.
SUPFAM; SSF143076; SSF143076; 1.
SUPFAM; SSF144246; SSF144246; 1.
SUPFAM; SSF50494; SSF50494; 1.
PROSITE; PS51442; M_PRO; 1.
PROSITE; PS51154; MACRO; 1.
PROSITE; PS51124; PEPTIDASE_C16; 1.
3: Inferred from homology;
Activation of host autophagy by virus; Complete proteome;
Host cytoplasm; Host membrane; Host-virus interaction; Hydrolase;
Membrane; Metal-binding; Protease; Repeat; Ribosomal frameshifting;
RNA-binding; Thiol protease; Transmembrane; Transmembrane helix; Zinc;
Zinc-finger.
CHAIN 1 3951 Replicase polyprotein 1a.
/FTId=PRO_0000338325.
CHAIN 1 673 Non-structural protein 2. {ECO:0000250}.
/FTId=PRO_0000338326.
CHAIN 674 2265 Non-structural protein 3. {ECO:0000250}.
/FTId=PRO_0000338327.
CHAIN 2266 2779 Non-structural protein 4. {ECO:0000250}.
/FTId=PRO_0000338328.
CHAIN 2780 3086 3C-like proteinase. {ECO:0000250}.
/FTId=PRO_0000338329.
CHAIN 3087 3379 Non-structural protein 6. {ECO:0000250}.
/FTId=PRO_0000338330.
CHAIN 3380 3462 Non-structural protein 7. {ECO:0000250}.
/FTId=PRO_0000338331.
CHAIN 3463 3672 Non-structural protein 8. {ECO:0000250}.
/FTId=PRO_0000338332.
CHAIN 3673 3783 Non-structural protein 9. {ECO:0000250}.
/FTId=PRO_0000338333.
CHAIN 3784 3928 Non-structural protein 10. {ECO:0000250}.
/FTId=PRO_0000338334.
CHAIN 3929 3951 Non-structural protein 11. {ECO:0000255}.
/FTId=PRO_0000338335.
TRANSMEM 1721 1741 Helical. {ECO:0000255}.
TRANSMEM 1751 1771 Helical. {ECO:0000255}.
TRANSMEM 1844 1864 Helical. {ECO:0000255}.
TRANSMEM 1869 1888 Helical. {ECO:0000255}.
TRANSMEM 2281 2301 Helical. {ECO:0000255}.
TRANSMEM 2560 2580 Helical. {ECO:0000255}.
TRANSMEM 2589 2609 Helical. {ECO:0000255}.
TRANSMEM 2612 2632 Helical. {ECO:0000255}.
TRANSMEM 2644 2664 Helical. {ECO:0000255}.
TRANSMEM 3101 3121 Helical. {ECO:0000255}.
TRANSMEM 3122 3142 Helical. {ECO:0000255}.
TRANSMEM 3152 3172 Helical. {ECO:0000255}.
TRANSMEM 3189 3209 Helical. {ECO:0000255}.
TRANSMEM 3220 3240 Helical. {ECO:0000255}.
TRANSMEM 3258 3278 Helical. {ECO:0000255}.
TRANSMEM 3297 3317 Helical. {ECO:0000255}.
DOMAIN 1003 1179 Macro. {ECO:0000255|PROSITE-
ProRule:PRU00490}.
DOMAIN 1236 1497 Peptidase C16. {ECO:0000255|PROSITE-
ProRule:PRU00444}.
DOMAIN 2780 3086 Peptidase C30. {ECO:0000255|PROSITE-
ProRule:PRU00772}.
ZN_FING 1353 1390 C4-type. {ECO:0000255|PROSITE-
ProRule:PRU00444}.
ZN_FING 3858 3878 {ECO:0000250}.
ZN_FING 3904 3917 {ECO:0000250}.
REGION 1721 1888 HD1.
REGION 2281 2664 HD2.
REGION 2885 3317 HD3.
ACT_SITE 1274 1274 For PL-PRO activity.
{ECO:0000255|PROSITE-ProRule:PRU00444}.
ACT_SITE 1437 1437 For PL-PRO activity.
{ECO:0000255|PROSITE-ProRule:PRU00444}.
ACT_SITE 2820 2820 For 3CL-PRO activity.
{ECO:0000255|PROSITE-ProRule:PRU00772}.
ACT_SITE 2922 2922 For 3CL-PRO activity.
{ECO:0000255|PROSITE-ProRule:PRU00772}.
SITE 673 674 Cleavage; by PL-PRO. {ECO:0000250}.
SITE 2265 2266 Cleavage; by PL-PRO. {ECO:0000250}.
SITE 2779 2780 Cleavage; by 3CL-PRO. {ECO:0000250}.
SITE 3086 3087 Cleavage; by 3CL-PRO. {ECO:0000250}.
SITE 3379 3380 Cleavage; by 3CL-PRO. {ECO:0000250}.
SITE 3462 3463 Cleavage; by 3CL-PRO. {ECO:0000250}.
SITE 3672 3673 Cleavage; by 3CL-PRO. {ECO:0000250}.
SITE 3783 3784 Cleavage; by 3CL-PRO. {ECO:0000250}.
SITE 3928 3929 Cleavage; by 3CL-PRO. {ECO:0000250}.
SEQUENCE 3951 AA; 441126 MW; 9B8B2E7E2545F50C CRC64;
MASSLKQGVS PKPRDVILVS KDIPEQLCDA LFFYTSHNPK DYADAFAVRQ KFDRSLQTGK
QFKFETVCGL FLLKGVDKIT PGVPAKVLKA TSKLADLEDI FGVSPLARKY RELLKTACQW
SLTVEALDVR AQTLDEIFDP TEILWLQVAA KIHVSSMAMR RLVGEVTAKV MDALGSNLSA
LFQIVKQQIA RIFQKALAIF ENVNELPQRI AALKMAFAKC ARSITVVVVE RTLVVKEFAG
TCLASINGAV AKFFEELPNG FMGSKIFTTL AFFKEAAVRV VENIPNAPRG TKGFEVVGNA
KGTQVVVRGM RNDLTLLDQK ADIPVEPEGW SAILDGHLCY VFRSGDRFYA APLSGNFALS
DVHCCERVVC LSDGVTPEIN DGLILAAIYS SFSVSELVTA LKKGEPFKFL GHKFVYAKDA
AVSFTLAKAA TIADVLRLFQ SARVIAEDVW SSFTEKSFEF WKLAYGKVRN LEEFVKTYVC
KAQMSIVILA AVLGEDIWHL VSQVIYKLGV LFTKVVDFCD KHWKGFCVQL KRAKLIVTET
FCVLKGVAQH CFQLLLDAIH SLYKSFKKCA LGRIHGDLLF WKGGVHKIVQ DGDEIWFDAI
DSVDVEDLGV VQEKSIDFEV CDDVTLPENQ PGHMVQIEDD GKNYMFFRFK KDENIYYTPM
SQLGAINVVC KAGGKTVTFG ETTVQEIPPP DVVPIKVSIE CCGEPWNTIF KKAYKEPIEV
DTDLTVEQLL SVIYEKMCDD LKLFPEAPEP PPFENVALVD KNGKDLDCIK SCHLIYRDYE
SDDDIEEEDA EECDTDSGEA EECDTNSECE EEDEDTKVLA LIQDPASIKY PLPLDEDYSV
YNGCIVHKDA LDVVNLPSGE ETFVVNNCFE GAVKPLPQKV VDVLGDWGEA VDAQEQLCQQ
EPLQHTFEEP VENSTGSSKT MTEQVVVEDQ ELPVVEQDQD VVVYTPTDLE VAKETAEEVD
EFILIFAVPK EEVVSQKDGA QIKQEPIQVV KPQREKKAKK FKVKPATCEK PKFLEYKTCV
GDLTVVIAKA LDEFKEFCIV NAANEHMTHG SGVAKAIADF CGLDFVEYCE DYVKKHGPQQ
RLVTPSFVKG IQCVNNVVGP RHGDNNLHEK LVAAYKNVLV DGVVNYVVPV LSLGIFGVDF
KMSIDAMREA FEGCTIRVLL FSLSQEHIDY FDVTCKQKTI YLTEDGVKYR SIVLKPGDSL
GQFGQVYAKN KIVFTADDVE DKEILYVPTT DKSILEYYGL DAQKYVIYLQ TLAQKWNVQY
RDNFLILEWR DGNCWISSAI VLLQAAKIRF KGFLTEAWAK LLGGDPTDFV AWCYASCTAK
VGDFSDANWL LANLAEHFDA DYTNAFLKKR VSCNCGIKSY ELRGLEACIQ PVRATNLLHF
KTQYSNCPTC GANNTDEVIE ASLPYLLLFA TDGPATVDCD EDAVGTVVFV GSTNSGHCYT
QAAGQAFDNL AKDRKFGKKS PYITAMYTRF AFKNETSLPV AKQSKGKSKS VKEDVSNLAT
SSKASFDNLT DFEQWYDSNI YESLKVQESP DNFDKYVSFT TKEDSKLPLT LKVRGIKSVV
DFRSKDGFIY KLTPDTDENS KAPVYYPVLD AISLKAIWVE GNANFVVGHP NYYSKSLHIP
TFWENAENFV KMGDKIGGVT MGLWRAEHLN KPNLERIFNI AKKAIVGSSV VTTQCGKLIG
KAATFIADKV GGGVVRNITD SIKGLCGITR GHFERKMSPQ FLKTLMFFLF YFLKASVKSV
VASYKTVLCK VVLATLLIVW FVYTSNPVMF TGIRVLDFLF EGSLCGPYKD YGKDSFDVLR
YCADDFICRV CLHDKDSLHL YKHAYSVEQV YKDAASGFIF NWNWLYLVFL ILFVKPVAGF
VIICYCVKYL VLNSTVLQTG VCFLDWFVQT VFSHFNFMGA GFYFWLFYKI YIQVHHILYC
KDVTCEVCKR VARSNRQEVS VVVGGRKQIV HVYTNSGYNF CKRHNWYCRN CDDYGHQNTF
MSPEVAGELS EKLKRHVKPT AYAYHVVDEA CLVDDFVNLK YKAATPGKDS ASSAVKCFSV
TDFLKKAVFL KEALKCEQIS NDGFIVCNTQ SAHALEEAKN AAIYYAQYLC KPILILDQAL
YEQLVVEPVS KSVIDKVCSI LSSIISVDTA ALNYKAGTLR DALLSITKDE EAVDMAIFCH
NHDVDYTGDG FTNVIPSYGI DTGKLTPRDR GFLINADASI ANLRVKNAPP VVWKFSELIK
LSDSCLKYLI SATVKSGVRF FITKSGAKQV IACHTQKLLV EKKAGGIVSG TFKCFKSYFK
WLLIFYILFT ACCSGYYYME VSKSFVHPMY DVNSTLHVEG FKVIDKGVLR EIVPEDTCFS
NKFVNFDAFW GRPYDNSRNC PIVTAVIDGD GTVATGVPGF VSWVMDGVMF IHMTQTERKP
WYIPTWFNRE IVGYTQDSII TEGSFYTSIA LFSARCLYLT ASNTPQLYCF NGDNDAPGAL
PFGSIIPHRV YFQPNGVRLI VPQQILHTPY VVKFVSDSYC RGSVCEYTRP GYCVSLNPQW
VLFNDEYTSK PGVFCGSTVR ELMFSMVSTF FTGVNPNIYM QLATMFLILV VVVLIFAMVI
KFQGVFKAYA TTVFITMLVW VINAFILCVH SYNSVLAVIL LVLYCYASLV TSRNTVIIMH
CWLVFTFGLI VPTWLACCYL GFIIYMYTPL FLWCYGTTKN TRKLYDGNEF VGNYDLAAKS
TFVIRGSEFV KLTNEIGDKF EAYLSAYARL KYYSGTGSEQ DYLQACRAWL AYALDQYRNS
GVEIVYTPPR YSIGVSRLQS GFKKLVSPSS AVEKCIVSVS YRGNNLNGLW LGDTIYCPRH
VLGKFSGDQW NDVLNLANNH EFEVTTQHGV TLNVVSRRLK GAVLILQTAV ANAETPKYKF
IKANCGDSFT IACAYGGTVV GLYPVTMRSN GTIRASFLAG ACGSVGFNIE KGVVNFFYMH
HLELPNALHT GTDLMGEFYG GYVDEEVAQR VPPDNLVTNN IVAWLYAAII SVKESSFSLP
KWLESTTVSV DDYNKWAGDN GFTPFSTSTA ITKLSAITGV DVCKLLRTIM VKNSQWGGDP
ILGQYNFEDE LTPESVFNQI GGVRLQSSFV RKATSWFWSR CVLACFLFVL CAIVLFTAVP
LKFYVYAAVI LLMAVLFISF TVKHVMAYMD TFLLPTLITV IIGVCAEVPF IYNTLISQVV
IFLSQWYDPV VFDTMVPWMF LPLVLYTAFK CVQGCYMNSF NTSLLMLYQF VKLGFVIYTS
SNTLTAYTEG NWELFFELVH TTVLANVSSN SLIGLFVFKC AKWMLYYCNA TYLNNYVLMA
VMVNCIGWLC TCYFGLYWWV NKVFGLTLGK YNFKVSVDQY RYMCLHKINP PKTVWEVFST
NILIQGIGGD RVLPIATVQA KLSDVKCTTV VLMQLLTKLN VEANSKMHVY LVELHNKILA
SDDVGECMDN LLGMLITLFC IDSTIDLSEY CDDILKRSTV LQSVTQEFSH IPSYAEYERA
KNLYEKVLVD SKNGGVTQQE LAAYRKAANI AKSVFDRDLA VQKKLDSMAE RAMTTMYKEA
RVTDRRAKLV SSLHALLFSM LKKIDSEKLN VLFDQASSGV VPLATVPIVC SNKLTLVIPD
PETWVKCVEG VHVTYSTVVW NIDTVIDADG TELHPTSTGS GLTYCISGAN IAWPLKVNLT
RNGHNKVDVV LQNNELMPHG VKTKACVAGV DQAHCSVESK CYYTNISGNS VVAAITSSNP
NLKVASFLNE AGNQIYVDLD PPCKFGMKVG VKVEVVYLYF IKNTRSIVRG MVLGAISNVV
VLQSKGHETE EVDAVGILSL CSFAVDPADT YCKYVAAGNQ PLGNCVKMLT VHNGSGFAIT
SKPSPTPDQD SYGGASVCLY CRAHIAHPGS VGNLDGRCQF KGSFVQIPTT EKDPVGFCLR
NKVCTVCQCW IGYGCQCDSL RQPKSSVQSV AGASDFDKNY LNGYGVAVRL G


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