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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN VOLTAGE-DEPENDENT ANION CHANNEL 1 (HVDAC1) IN C222 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 :  3.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Membrane Protein, Cell-Free Synthesis, Beta-Barrel Structure (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
1HEX1Ligand/IonHEXANE
2LNK2Ligand/IonPENTANE
3OCT4Ligand/IonN-OCTANE
4SPD2Ligand/IonSPERMIDINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:7 , LEU A:10 , GLN A:154 , ASN A:183binding site for residue SPD A 301
2AC2SOFTWAREASN A:214 , PHE B:219 , OCT B:302binding site for residue OCT A 302
3AC3SOFTWARESER A:167 , PHE A:169binding site for residue OCT A 303
4AC4SOFTWARETYR A:153binding site for residue LNK A 304
5AC5SOFTWAREARG A:120binding site for residue HEX A 306
6AC6SOFTWARETYR B:7 , LEU B:10 , ARG B:15 , HIS B:181 , THR B:182 , ASN B:183binding site for residue SPD B 301
7AC7SOFTWARELEU A:208 , OCT A:302binding site for residue OCT B 302
8AC8SOFTWAREPHE B:190 , TRP B:210 , GLY B:213binding site for residue OCT B 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5XDO)

(-) 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:283
                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhh.....eeeeeeee......eeeeeeeee.....eeeeeeeeee.....eeeeeeee....eeeeeeee......eeeeeeeee........eeeeeeee...eeeeeeee......eeeeeeeeee..eeeeeeeeee.....eeeeeeeeeee...eeeeeeee...eeeeeeeeeee..eeeeeeeeee...eeeeeeeeeeeeee..eeeeeeee...eeeeeeeeeee..eeeeeeeeee.........eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5xdo A   1 MAVPPTYADLGKSARDVFTKGYGFGLIKLDLKTKSENGLEFTSSGSANTETTKVTGSLETKYRWTEYGLTFTEKWNTDNTLGTEITVEDQLARGLKLTFDSSFSPNTGKKNAKIKTGYKREHINLGCDMDFDIAGPSIRGALVLGYEGWLAGYQMNFETAKSRVTQSNFAVGYKTDEFQLHTNVNDGTEFGGSIYQKVNKKLETAVNLAWTAGNSNTRFGIAAKYQIDPDACFSAKVNNSSLIGLGYTQTLKPGIKLTLSALLDGKNVNAGGHKLGLGLEFQA 283
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280   


Chain B from PDB  Type:PROTEIN  Length:258
                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhhhhhhh......eeeeee...eeeeee......eeeeeeeeeee....eeeeeee.....eeeeeeee......eeeeee..eeeeeee...eeeeeee..eeeeeeee..eeeeeeeee......eeeeeeeeeee...eeeeeeee...eeeeeeee.....eeeeeeeeee.....eeeeeeeee.....eeeeeeee...eeeeeeeeeee..eeeeeeeeee.........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5xdo B   1 MAVPPTYADLGKSARDVFTKGYGFGLIKLDLKTKFTSSGSANTETTKVTGSLETKYRWTEYGLTFTEKWNTDNTLGTEITVEDQLARGLKLTFDSAKIKTGYKREHINLGCDMDIRGALVLGYEGWLAGYQMNFETAKSRVTQSNFAVGYKTDEFQLHTNVNDGTEFGGSIYQKVNKKLETAVNLAWTAGNSNTRFGIAAKYQIDPDACFSAKVNNSSLIGLGYTQTLKPGIKLTLSALLDGKNVNAGGHKLGLGLEF 281
                                    10        20        30   ||   46        56        66        76        86        96    || 116       126   ||  143       153       163       173       183       193       203       213       223       233       243       253       263       273        
                                                            34|                                                         101|               130|                                                                                                                                               
                                                             41                                                          112                138
   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 5XDO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (39, 39)

Asymmetric/Biological Unit(hide GO term definitions)

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  5xdo
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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 5xdn

(-) Related Entries Specified in the PDB File

5xdn