Cyclic Peptide DataBank (CPDB)
Browse and visualize 3D structures of polypeptides
Browse and visualize 3D structures of polypeptides
| PDB ID | 9DBN Go to RCSB ➚ |
| Title | Tarantula venom peptide Protoxin-I bound to full-length human voltage-gated sodium channel 1.8 (NaV1.8) |
| Method | ELECTRON MICROSCOPY |
| Resolution | 2.76 Å |
| Release Date | 2025-02-19 |
| Authors | Neumann, B.; McCarthy, S.; Gonen, S. |
| Source Organism | Homo sapiens, Thrixopelma pruriens |
| Expression Host | Homo sapiens |
| Gene Names | SCN10A |
| Keywords | ion channel, MEMBRANE PROTEIN |
| Molecular Weight | 240.70 kDa |
| Entity Count | Protein: 2, Nucleic Acid: 0, NA Hybrid: 0 |
| Disulfide Bond | B2-B16;B9-B21;B15-B28 |
| Other Links | Yes |
| Peptide Chains | B |
| Protein Chains | A |
| Peptide Lengths | 35 |
| Protein Lengths | 2001 |
| 1 | DYKDDDDKSA WSHPQFEKGG GSGGGSGGSA WSHPQFEKEN LYFQSMEFPI GSLETNNFRR |
| 61 | FTPESLVEIE KQIAAKQGTK KAREKHREQK DQEEKPRPQL DLKACNQLPK FYGELPAELI |
| 121 | GEPLEDLDPF YSTHRTFMVL NKGRTISRFS ATRALWLFSP FNLIRRTAIK VSVHSWFSLF |
| 181 | ITVTILVNCV CMTRTDLPEK IEYVFTVIYT FEALIKILAR GFCLNEFTYL RDPWNWLDFS |
| 241 | VITLAYVGTA IDLRGISGLR TFRVLRALKT VSVIPGLKVI VGALIHSVKK LADVTILTIF |
| 301 | CLSVFALVGL QLFKGNLKNK CVKNDMAVNE TTNYSSHRKP DIYINKRGTS DPLLCGNGSD |
| 361 | SGHCPDGYIC LKTSDNPDFN YTSFDSFAWA FLSLFRLMTQ DSWERLYQQT LRTSGKIYMI |
| 421 | FFVLVIFLGS FYLVNLILAV VTMAYEEQNQ ATTDEIEAKE KKFQEALEML RKEQEVLAAL |
| 481 | GIDTTSLHSH NGSPLTSKNA SERRHRIKPR VSEGSTEDNK SPRSDPYNQR RMSFLGLASG |
| 541 | KRRASHGSVF HFRSPGRDIS LPEGVTDDGV FPGDHESHRG SLLLGGGAGQ QGPLPRSPLP |
| 601 | QPSNPDSRHG EDEHQPPPTS ELAPGAVDVS AFDAGQKKTF LSAEYLDEPF RAQRAMSVVS |
| 661 | IITSVLEELE ESEQKCPPCL TSLSQKYLIW DCCPMWVKLK TILFGLVTDP FAELTITLCI |
| 721 | VVNTIFMAME HHGMSPTFEA MLQIGNIVFT IFFTAEMVFK IIAFDPYYYF QKKWNIFDCI |
| 781 | IVTVSLLELG VAKKGSLSVL RSFRLLRVFK LAKSWPTLNT LIKIIGNSVG ALGNLTIILA |
| 841 | IIVFVFALVG KQLLGENYRN NRKNISAPHE DWPRWHMHDF FHSFLIVFRI LCGEWIENMW |
| 901 | ACMEVGQKSI CLILFLTVMV LGNLVVLNLF IALLLNSFSA DNLTAPEDDG EVNNLQVALA |
| 961 | RIQVFGHRTK QALCSFFSRS CPFPQPKAEP ELVVKLPLSS SKAENHIAAN TARGSSGGLQ |
| 1021 | APRGPRDEHS DFIANPTVWV SVPIAEGESD LDDLEDDGGE DAQSFQQEVI PKGQQEQLQQ |
| 1081 | VERCGDHLTP RSPGTGTSSE DLAPSLGETW KDESVPQVPA EGVDDTSSSE GSTVDCLDPE |
| 1141 | EILRKIPELA DDLEEPDDCF TEGCIRHCPC CKLDTTKSPW DVGWQVRKTC YRIVEHSWFE |
| 1201 | SFIIFMILLS SGSLAFEDYY LDQKPTVKAL LEYTDRVFTF IFVFEMLLKW VAYGFKKYFT |
| 1261 | NAWCWLDFLI VNISLISLTA KILEYSEVAP IKALRTLRAL RPLRALSRFE GMRVVVDALV |
| 1321 | GAIPSIMNVL LVCLIFWLIF SIMGVNLFAG KFWRCINYTD GEFSLVPLSI VNNKSDCKIQ |
| 1381 | NSTGSFFWVN VKVNFDNVAM GYLALLQVAT FKGWMDIMYA AVDSREVNMQ PKWEDNVYMY |
| 1441 | LYFVIFIIFG GFFTLNLFVG VIIDNFNQQK KKLGGQDIFM TEEQKKYYNA MKKLGSKKPQ |
| 1501 | KPIPRPLNKF QGFVFDIVTR QAFDITIMVL ICLNMITMMV ETDDQSEEKT KILGKINQFF |
| 1561 | VAVFTGECVM KMFALRQYYF TNGWNVFDFI VVVLSIASLI FSAILKSLQS YFSPTLFRVI |
| 1621 | RLARIGRILR LIRAAKGIRT LLFALMMSLP ALFNIGLLLF LVMFIYSIFG MSSFPHVRWE |
| 1681 | AGIDDMFNFQ TFANSMLCLF QITTSAGWDG LLSPILNTGP PYCDPNLPNS NGTRGDCGSP |
| 1741 | AVGIIFFTTY IIISFLIVVN MYIAVILENF NVATEESTEP LSEDDFDMFY ETWEKFDPEA |
| 1801 | TQFITFSALS DFADTLSGPL RIPKPNRNIL IQMDLPLVPG DKIHCLDILF AFTKNVLGES |
| 1861 | GELDSLKANM EEKFMATNLS KSSYEPIATT LRWKQEDISA TVIQKAYRSY VLHRSMALSN |
| 1921 | TPCVPRAEEE AASLPDEGFV AFTANENCVL PDKSETASAT SFPPSYESVT RGLSDRVNMR |
| 1981 | TSSSIQNEDE ATSMELIAPG P |
| 1 | ECRYWLGGCS AGQTCCKHLV CSRRHGWCVW DGTFS |
Structural basis of inhibition of human Na V 1.8 by the tarantula venom peptide Protoxin-I.
Nat Commun, 2025
| ID | Name | Formula | Molecular Weight |
|---|---|---|---|
| CLR | CHOLESTEROL | C27 H46 O | 386.654 |
| PCW | 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE | C44 H85 N O8 P | 787.121 |
| LPE | 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE | C26 H57 N O6 P | 510.708 |
| P5S | O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine | C42 H82 N O10 P | 792.075 |
Assembly ID: 1
Details: author_defined_assembly
Oligomeric State: Hetero 2-mer
Stoichiometry: A1, B1