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(-) Description

Title :  STRUCTURE OF NAVMS IN COMPLEX WITH CHANNEL BLOCKING COMPOUND
 
Authors :  C. E. Naylor, C. Bagneris, B. A. Wallace
Date :  04 Apr 14  (Deposition) - 04 Jun 14  (Release) - 06 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.91
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  C,D  (2x)
Keywords :  Channel Blocking Compound, Sodium Channel, Pore, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Bagneris, P. G. Decaen, C. E. Naylor, D. C. Pryde, I. Nobeli, D. E. Clapham, B. A. Wallace
Prokaryotic Navms Channel As A Structural And Functional Model For Eukaryotic Sodium Channel Antagonism.
Proc. Natl. Acad. Sci. Usa V. 111 8428 2014
PubMed-ID: 24850863  |  Reference-DOI: 10.1073/PNAS.1406855111
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ION TRANSPORT PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: C41
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MMC1_0798
    Organism Scientific: MAGNETOCOCCUS SP.
    Organism Taxid: 156889
    Strain: MC-1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): AB  
Biological Unit 2 (2x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
112P2Ligand/IonDODECAETHYLENE GLYCOL
22CV4Ligand/IonHEGA-10
3BR4Ligand/IonBROMIDE ION
4NA4Ligand/IonSODIUM ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
112P4Ligand/IonDODECAETHYLENE GLYCOL
22CV4Ligand/IonHEGA-10
3BR-1Ligand/IonBROMIDE ION
4NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
112P-1Ligand/IonDODECAETHYLENE GLYCOL
22CV4Ligand/IonHEGA-10
3BR-1Ligand/IonBROMIDE ION
4NA-1Ligand/IonSODIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:153 , HIS A:192binding site for residue 12P A 301
2AC2SOFTWAREMET A:189 , PRO A:193 , TRP A:196 , HOH A:461 , SER B:165 , LYS B:166 , TYR B:169 , HOH B:435 , HOH B:458binding site for residue 2CV B 301
3AC3SOFTWARESER A:165 , TYR A:169 , PHE A:172 , ASN B:194 , TRP B:196 , HOH B:401 , HOH B:403binding site for residue 2CV B 302
4AC4SOFTWARETYR B:153 , VAL B:197 , HOH B:415binding site for residue 12P B 303
5AC5SOFTWAREASN C:194 , TRP C:196 , HOH C:430 , PHE D:142 , SER D:165binding site for residue 2CV C 301
6AC6SOFTWAREHOH C:473binding site for residue BR C 302
7AC7SOFTWAREPHE C:142 , SER C:165 , TRP D:196 , HOH D:409 , HOH D:458binding site for residue 2CV D 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P9P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4P9P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P9P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P9P)

(-) Exons   (0, 0)

(no "Exon" information available for 4P9P)

(-) 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:92
                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 4p9p A 131 VGSVAALLTVVFYIAAVMATNLYGATFPEWFGDLSKSLYTLFQVMTLESWSMGIVRPVMNVHPNAWVFFIPFIMLTTFTVLNLFIGIIVDAM 222
                                   140       150       160       170       180       190       200       210       220  


Chain B from PDB  Type:PROTEIN  Length:90
                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 4p9p B 131 VGSVAALLTVVFYIAAVMATNLYGATFPEWFGDLSKSLYTLFQVMTLESWSMGIVRPVMNVHPNAWVFFIPFIMLTTFTVLNLFIGIIVD 220
                                   140       150       160       170       180       190       200       210       220


Chain C from PDB  Type:PROTEIN  Length:91
                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh......hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 4p9p C 130 GVGSVAALLTVVFYIAAVMATNLYGATFPEWFGDLSKSLYTLFQVMTLESWSMGIVRPVMNVHPNAWVFFIPFIMLTTFTVLNLFIGIIVD 220
                                   139       149       159       169       179       189       199       209       219 


Chain D from PDB  Type:PROTEIN  Length:91
                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 4p9p D 130 GVGSVAALLTVVFYIAAVMATNLYGATFPEWFGDLSKSLYTLFQVMTLESWSMGIVRPVMNVHPNAWVFFIPFIMLTTFTVLNLFIGIIVD 220
                                   139       149       159       169       179       189       199       209       219
   Legend:   → Mismatch (orange background)
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  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 4P9P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P9P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P9P)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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        A0L5S6_MAGMM | A0L5S6: 3zjz 4cbc 4f4l 4oxs 4p2z 4p30 4p9o 4pa3 4pa4 4pa6 4pa7 4pa9 4x88 4x89 4x8a 5bzb 5hvd 5hvx

(-) Related Entries Specified in the PDB File

4cbc NATIVE CHANNEL
4p30 COMPLEX OF CHANNEL BLOCKING COMPOUND AND T207A/F214A MUTANT CHANNEL
4p90 COMPLEX IN THE PRESENCE OF ALTERNATIVE CHANNEL BLOCKING COMPOUND