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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN VOLTAGE-DEPENDENT ANION CHANNEL 1 (HVDAC1) IN P22121 SPACE GROUP
 
Authors :  T. Hosaka, T. Kimura-Someya, M. Shirouzu
Date :  28 Mar 17  (Deposition) - 28 Jun 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Membrane Protein, Beta-Barrel Structure, Cell-Free Synthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Hosaka, M. Okazaki, T. Kimura-Someya, Y. Ishizuka-Katsura, K. Ito S. Yokoyama, K. Dodo, M. Sodeoka, M. Shirouzu
Crystal Structural Characterization Reveals Novel Oligomeri Interactions Of Human Voltage-Dependent Anion Channel 1
Protein Sci. 2017
PubMed-ID: 28608415  |  Reference-DOI: 10.1002/PRO.3211

(-) Compounds

Molecule 1 - VOLTAGE-DEPENDENT ANION-SELECTIVE CHANNEL PROTEIN 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: VDAC1, VDAC
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HVDAC1,OUTER MITOCHONDRIAL MEMBRANE PROTEIN PORIN 1, PLASMALEMMAL PORIN,PORIN 31HL,PORIN 31HM

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
1D102Ligand/IonDECANE
2D122Ligand/IonDODECANE
3HEX4Ligand/IonHEXANE
4OCT1Ligand/IonN-OCTANE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:146 , ASN B:238 , SER B:241binding site for residue D12 A 301
2AC2SOFTWAREMET A:129 , D10 B:301binding site for residue HEX A 302
3AC3SOFTWAREILE A:138 , PHE A:157 , PHE B:178binding site for residue OCT A 303
4AC4SOFTWAREHEX A:302 , TYR B:173binding site for residue D10 B 301
5AC5SOFTWAREPHE A:190 , TYR B:118binding site for residue D10 B 302
6AC6SOFTWAREARG A:93 , TYR A:118 , TRP B:210binding site for residue D12 B 303
7AC7SOFTWAREGLU B:73 , LEU B:81 , THR B:83binding site for residue HEX B 304
8AC8SOFTWAREPHE B:169binding site for residue HEX B 305
9AC9SOFTWARETHR B:204binding site for residue HEX B 306

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5XDN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5XDN)

(-) 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:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhh.....eeeeeee...eeeeeeeeee.....eeeeeeeeeee....eeeeeee.....eeeeeeee......eeeeeeeee....eeeeeeeeeee..eeeeeeeee.....eeeeeeeeee..eeeeeeeeee....eeeeeeeeeeeee..eeeeeeee...eeeeeeee.....eeeeeeeeee......eeeeeeeeeee..eeeeeeee...eeeeeeeeeee..eeeeeeeeee.......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5xdn A  -1 GSMAVPPTYADLGKSARDVFTKGYGFGLIKLDLKTKGLEFTSSGSANTETTKVTGSLETKYRWTEYGLTFTEKWNTDNTLGTEITVEDQLARGLKLTFDSSFSPGKKNAKIKTGYKREHINLGCDMDFDIAGPSIRGALVLGYEGWLAGYQMNFETAKSRVTQSNFAVGYKTDEFQLHTNVNDGTEFGGSIYQKVNKKLETAVNLAWTAGNSNTRFGIAAKYQIDPDACFSAKVNNSSLIGLGYTQTLKPGIKLTLSALLDGKNAGGHKLGLGLEFQA 283
                                     8        18        28     || 41        51        61        71        81        91       101   ||  113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263   ||  275        
                                                              34|                                                                105|                                                                                                                                                            267|             
                                                               38                                                                 108                                                                                                                                                             270             


Chain B from PDB  Type:PROTEIN  Length:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhh......eeeeeeee...eeeeeeeeee.....eeeeeeeeeee....eeeeeeee....eeeeeeee......eeeeee.......eeeeeeee..eeeeeeee..eeeeeeeeee..eeeeeeeeee....eeeeeeeeeeee...eeeeeeee...eeeeeeee.....eeeeeeeeee......eeeeeeeeeee..eeeeeeee...eeeeeeeeeee..eeeeeeeeee......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5xdn B  -1 GSMAVPPTYADLGKSARDVFTKGYGFGLIKLDLKTKSGLEFTSSGSANTETTKVTGSLETKYRWTEYGLTFTEKWNTDNTLGTEITVEDQLARGLKLTFDSSFSKNAKIKTGYKREHINLGCDMDFPSIRGALVLGYEGWLAGYQMNFETAKSRVTQSNFAVGYKTDEFQLHTNVNDGTEFGGSIYQKVNKKLETAVNLAWTAGNSNTRFGIAAKYQIDPDACFSAKVNNSSLIGLGYTQTLKPGIKLTLSALLDGKAGGHKLGLGLEFQA 283
                                     8        18        28      ||40        50        60        70        80        90       100   ||  115       125     ||139       149       159       169       179       189       199       209       219       229       239       249       259      |272       282 
                                                               35|                                                               104|                  131|                                                                                                                               266|             
                                                                38                                                                110                   136                                                                                                                                270
   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 5XDN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (39, 39)

Asymmetric/Biological Unit(hide GO term definitions)

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  VDAC1_HUMAN | P21796
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 Related Entries

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

UniProtKB/Swiss-Prot
        VDAC1_HUMAN | P21796: 2jk4 2k4t 5jdp 5xdo

(-) Related Entries Specified in the PDB File

5xdo