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(-) Description

Title :  HUMAN NAV1.7-VSD4-NAVAB IN COMPLEX WITH GX-936.
 
Authors :  S. Ahuja, S. Mukund, M. A. Starovasnik, C. M. Koth, J. Payandeh
Date :  03 Nov 15  (Deposition) - 23 Dec 15  (Release) - 30 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.53
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Membrane Protein, Ion Channel, Voltage-Gated Sodium Channel, Small Molecule Antagonist, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ahuja, S. Mukund, L. Deng, K. Khakh, E. Chang, H. Ho, S. Shriver, C. Young, S. Lin, J. P. Johnson, P. Wu, J. Li, M. Coons, C. Tam, B. Brillantes, H. Sampang, K. Mortara, K. K. Bowman, K. R. Clark, A. Estevez, Z. Xie, H. Verschoof, M. Grimwood, C. Dehnhardt, J. C. Andrez, T. Focken, D. P. Sutherlin, B. S. Safina, M. A. Starovasnik, D. F. Ortwine, Y. Franke, C. J. Cohen, D. H. Hackos, C. M. Koth, J. Payandeh
Structural Basis Of Nav1. 7 Inhibition By An Isoform-Selective Small-Molecule Antagonist.
Science V. 350 C5464 2015
PubMed-ID: 26680203  |  Reference-DOI: 10.1126/SCIENCE.AAC5464

(-) Compounds

Molecule 1 - CHIMERA OF BACTERIAL ION TRANSPORT PROTEIN AND HUMAN SODIUM CHANNEL PROTEIN TYPE 9 SUBUNIT ALPHA
    Chains: A, B, C, D
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Gene: ABU_1752, SCN9A, NENA
    Organism Scientific: ARCOBACTER BUTZLERI, HOMO SAPIENS
    Organism Taxid: 367737, 9606
    Strain: RM4018
    Synonym: EUROENDOCRINE SODIUM CHANNEL,HNE-NA,PERIPHERAL SODIUM CHANNEL 1,PN1,SODIUM CHANNEL PROTEIN TYPE IX SUBUNIT ALPHA,VOLTAGE- GATED SODIUM CHANNEL SUBUNIT ALPHA NAV1.7

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 25)

Asymmetric/Biological Unit (2, 25)
No.NameCountTypeFull Name
15P24Ligand/Ion3-CYANO-4-[2-[2-(1-ETHYLAZETIDIN-3-YL)PYRAZOL-3-YL]-4-(TRIFLUOROMETHYL)PHENOXY]-~{N}-(1,2,4-THIADIAZOL-5-YL)BENZENESULFONAMIDE
2PX421Ligand/Ion1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:1654 , PHE A:1655 , TYR A:1694 , PRO A:1695 , TYR A:1696 , ARG D:1599binding site for residue PX4 A 1801
02AC2SOFTWARETHR A:1665 , GLY A:1667 , GLU A:1668 , PHE A:1670 , TYR A:1671 , PRO B:1695 , TRP B:1698binding site for residue PX4 A 1802
03AC3SOFTWAREGLN A:1618binding site for residue PX4 A 1804
04AC4SOFTWAREGLN A:1530 , GLU A:1534 , 5P2 A:1808binding site for residue PX4 A 1807
05AC5SOFTWAREGLU A:1534 , TYR A:1537 , TRP A:1538 , ASN A:1540 , VAL A:1541 , GLY A:1581 , MET A:1582 , PHE A:1583 , ALA A:1585 , ASP A:1586 , PHE A:1598 , ARG A:1602 , ALA A:1604 , ARG A:1605 , ARG A:1608 , PX4 A:1807binding site for residue 5P2 A 1808
06AC6SOFTWARETHR A:1596 , ARG A:1599 , TYR B:1694 , PRO B:1695 , TYR B:1696 , ALA B:1697binding site for residue PX4 B 1801
07AC7SOFTWARETHR B:1665 , GLY B:1667 , GLU B:1668 , PHE B:1670 , TYR B:1671 , MET C:1691 , PRO C:1695 , TRP C:1698binding site for residue PX4 B 1802
08AC8SOFTWAREGLN B:1618binding site for residue PX4 B 1803
09AC9SOFTWAREMET B:1677binding site for residue PX4 B 1804
10AD1SOFTWAREGLU B:1534 , ASP B:1586 , 5P2 B:1806binding site for residue PX4 B 1805
11AD2SOFTWAREGLU B:1534 , TYR B:1537 , TRP B:1538 , ASN B:1540 , VAL B:1541 , GLY B:1581 , MET B:1582 , PHE B:1583 , ALA B:1585 , ASP B:1586 , PHE B:1598 , ARG B:1602 , ARG B:1605 , ARG B:1608 , PX4 B:1805binding site for residue 5P2 B 1806
12AD3SOFTWARETHR B:1596 , TYR C:1694 , PRO C:1695 , TYR C:1696binding site for residue PX4 C 1801
13AD4SOFTWARETYR C:1645 , THR C:1665 , GLY C:1667 , GLU C:1668 , PHE C:1670 , TYR D:1696 , TRP D:1698binding site for residue PX4 C 1802
14AD5SOFTWAREGLN C:1618binding site for residue PX4 C 1803
15AD6SOFTWAREGLU C:1534 , TRP C:1538 , 5P2 C:1805binding site for residue PX4 C 1804
16AD7SOFTWARETYR C:1537 , TRP C:1538 , ASN C:1540 , GLY C:1581 , MET C:1582 , PHE C:1583 , ALA C:1585 , ASP C:1586 , GLU C:1589 , THR C:1590 , PHE C:1598 , ARG C:1602 , ALA C:1604 , ARG C:1605 , ARG C:1608 , PX4 C:1804binding site for residue 5P2 C 1805
17AD8SOFTWAREMET A:1691 , TRP A:1698 , PHE D:1644 , GLY D:1667 , GLU D:1668 , PHE D:1670binding site for residue PX4 D 1801
18AD9SOFTWAREARG C:1599 , PHE D:1655 , TYR D:1694 , PRO D:1695 , TYR D:1696binding site for residue PX4 D 1802
19AE1SOFTWAREGLU D:1534 , 5P2 D:1806binding site for residue PX4 D 1805
20AE2SOFTWAREGLU D:1534 , TYR D:1537 , TRP D:1538 , ASN D:1540 , VAL D:1541 , SER D:1578 , GLY D:1581 , MET D:1582 , PHE D:1583 , ALA D:1585 , ASP D:1586 , PHE D:1598 , ARG D:1602 , ALA D:1604 , ARG D:1605 , ARG D:1608 , PX4 D:1805binding site for residue 5P2 D 1806

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EK0)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Arg A:-3 -Gly A:-2
2Gly A:1527 -Gln A:1528
3Gly B:1527 -Gln B:1528
4Gly C:1527 -Gln C:1528
5Gly D:1527 -Gln D:1528

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EK0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EK0)

(-) Exons   (0, 0)

(no "Exon" information available for 5EK0)

(-) 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:250
                                                                                                                                                                                                                                                                                           
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ek0 A   -4 PRGSHMYLRITNIVESSFFTKFIIYLIVLNMVTMMVEKEGQSQHMTEVLYWINVVFIILFTIEIILRIYVHRISFFKDPWSLFDFVVVIISIVGMFLADLIETYFVSPTLFRVIRLARIGRILRLVTAVPQMRKIVSALISVIPGMLSVIALMTLFFYIFAIMATQLFGERFPEWFGTLGESFYTLFQVMTLESWSMGIVRPLMEVYPYAWVFFIPFIFVVTFVMINLVVAIIVDAMAILNQKEEQHIID 1737
                                ||1497      1507      1517      1527      1537      1547      1557      1567      1577      1587      1597      1607      1617      1627      1637      1647      1657      1667      1677      1687      1697      1707      1717      1727      1737
                                0|                                                                                                                                                                                                                                                    
                              1493                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:245
                                                                                                                                                                                                                                                                                      
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh..hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ek0 B 1493 MYLRITNIVESSFFTKFIIYLIVLNMVTMMVEKEGQSQHMTEVLYWINVVFIILFTIEIILRIYVHRISFFKDPWSLFDFVVVIISIVGMFLADLIETYFVSPTLFRVIRLARIGRILRLVTAVPQMRKIVSALISVIPGMLSVIALMTLFFYIFAIMATQLFGERFPEWFGTLGESFYTLFQVMTLESWSMGIVRPLMEVYPYAWVFFIPFIFVVTFVMINLVVAIIVDAMAILNQKEEQHIID 1737
                                  1502      1512      1522      1532      1542      1552      1562      1572      1582      1592      1602      1612      1622      1632      1642      1652      1662      1672      1682      1692      1702      1712      1722      1732     


Chain C from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                   
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ek0 C 1493 MYLRITNIVESSFFTKFIIYLIVLNMVTMMVEKEGQSQHMTEVLYWINVVFIILFTIEIILRIYVHRISFFKDPWSLFDFVVVIISIVGMFLADLIETYPTLFRVIRLARIGRILRLVTAVPQMRKIVSALISVIPGMLSVIALMTLFFYIFAIMATQLFGERFPEWFGTLGESFYTLFQVMTLESWSMGIVRPLMEVYPYAWVFFIPFIFVVTFVMINLVVAIIVDAMAILNQKEEQHIID 1737
                                  1502      1512      1522      1532      1542      1552      1562      1572      1582      1595      1605      1615      1625      1635      1645      1655      1665      1675      1685      1695      1705      1715      1725      1735  
                                                                                                                           1591|                                                                                                                                              
                                                                                                                            1595                                                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                   
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ek0 D 1493 MYLRITNIVESSFFTKFIIYLIVLNMVTMMVEKEGQSQHMTEVLYWINVVFIILFTIEIILRIYVHRISFFKDPWSLFDFVVVIISIVGMFLADLIETYPTLFRVIRLARIGRILRLVTAVPQMRKIVSALISVIPGMLSVIALMTLFFYIFAIMATQLFGERFPEWFGTLGESFYTLFQVMTLESWSMGIVRPLMEVYPYAWVFFIPFIFVVTFVMINLVVAIIVDAMAILNQKEEQHIID 1737
                                  1502      1512      1522      1532      1542      1552      1562      1572      1582      1595      1605      1615      1625      1635      1645      1655      1665      1675      1685      1695      1705      1715      1725      1735  
                                                                                                                           1591|                                                                                                                                              
                                                                                                                            1595
   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  (0, 0)

(no "SCOP Domain" information available for 5EK0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EK0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EK0)

(-) Gene Ontology  (26, 32)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        A8EVM5_ARCB4 | A8EVM5: 3rvy 3rvz 3rw0 4ekw 4ms2 4mtf 4mtg 4mto 4mvm 4mvo 4mvq 4mvr 4mvs 4mvu 4mvz 4mw3 4mw8 5klb 5klg 5kls 5kmd 5kmf 5kmh 5vb2 5vb8

(-) Related Entries Specified in the PDB File

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