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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN BST2 CYTOPLASMIC DOMAIN AND THE HIV-1 VPU CYTOPLASMIC DOMAIN BOUND TO THE CLATHRIN ADAPTOR PROTEIN COMPLEX 1 (AP1) CORE
 
Authors :  X. Jia, Y. Xiong
Date :  25 Mar 14  (Deposition) - 21 May 14  (Release) - 11 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  B,G,M,S,T,V
Keywords :  Bst2, Tetherin, Vpu, Hiv, Clathrin, Ap1, Antiviral, Restriction Factor, Antagonism, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Jia, E. Weber, A. Tokarev, M. Lewinski, M. Rizk, M. Suarez, J. Guatelli, Y. Xiong
Structural Basis Of Hiv-1 Vpu-Mediated Bst2 Antagonism Via Hijacking Of The Clathrin Adaptor Protein Complex 1.
Elife V. 3 02362 2014
PubMed-ID: 24843023  |  Reference-DOI: 10.7554/ELIFE.02362

(-) Compounds

Molecule 1 - AP-1 COMPLEX SUBUNIT GAMMA-1
    ChainsG
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentBST2/TETHEIRN CYTOPLASMIC DOMAIN, UNP RESIDUES 1-613
    GeneAP1G1, ADTG, CLAPG1
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymADAPTER-RELATED PROTEIN COMPLEX 1 SUBUNIT GAMMA-1,ADAPTOR PROTEIN COMPLEX AP-1 SUBUNIT GAMMA-1,CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 GAMMA-1 LARGE CHAIN,GAMMA-ADAPTIN,GAMMA1-ADAPTIN,GOLGI ADAPTOR HA1/AP1 ADAPTIN SUBUNIT GAMMA-1
 
Molecule 2 - AP-1 COMPLEX SUBUNIT SIGMA-1A
    ChainsS
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentHIV-1 VPU CYTOPLASMIC DOMAIN
    GeneAP1S1, AP19, CLAPS1
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymADAPTER-RELATED PROTEIN COMPLEX 1 SUBUNIT SIGMA-1A,ADAPTOR PROTEIN COMPLEX AP-1 SUBUNIT SIGMA-1A,CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 SIGMA-1A SMALL CHAIN,CLATHRIN COAT ASSEMBLY PROTEIN AP19, GOLGI ADAPTOR HA1/AP1 ADAPTIN SIGMA-1A SUBUNIT,HA1 19 KDA SUBUNIT, SIGMA 1A SUBUNIT OF AP-1 CLATHRIN,SIGMA-ADAPTIN 1A,SIGMA1A-ADAPTIN
 
Molecule 3 - AP-1 COMPLEX SUBUNIT MU-1
    ChainsM
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentCLATHRIN ADAPTOR PROTEIN COMPLEX 1 (AP1) CORE, UNP RESIDUES 1-421
    GeneAP1M1, CLTNM
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymAP-MU CHAIN FAMILY MEMBER MU1A,ADAPTER-RELATED PROTEIN COMPLEX 1 SUBUNIT MU-1,ADAPTOR PROTEIN COMPLEX AP-1 SUBUNIT MU-1, CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 MU-1 MEDIUM CHAIN 1,CLATHRIN COAT ASSEMBLY PROTEIN AP47,CLATHRIN COAT-ASSOCIATED PROTEIN AP47,GOLGI ADAPTOR HA1/AP1 ADAPTIN MU-1 SUBUNIT,MU-ADAPTIN 1,MU1A-ADAPTIN
 
Molecule 4 - AP-1 COMPLEX SUBUNIT BETA-1
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentUNP RESIDUES 1-584
    GeneAP1B1, ADTB1, BAM22, CLAPB2
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymADAPTER-RELATED PROTEIN COMPLEX 1 SUBUNIT BETA-1,ADAPTOR PROTEIN COMPLEX AP-1 SUBUNIT BETA-1,BETA-1-ADAPTIN,BETA-ADAPTIN 1, CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 BETA LARGE CHAIN,GOLGI ADAPTOR HA1/AP1 ADAPTIN BETA SUBUNIT
 
Molecule 5 - PROTEIN VPU
    ChainsV
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentUNP RESIDUES 21-81
    GeneVPU
    Organism CommonHIV-1
    Organism ScientificHUMAN IMMUNODEFICIENCY VIRUS TYPE 1 GROUP M SUBTYPE B
    Organism Taxid11691
    StrainISOLATE SF162
    SynonymU ORF PROTEIN,VIRAL PROTEIN U
 
Molecule 6 - BONE MARROW STROMAL ANTIGEN 2
    ChainsT
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentUNP RESIDUES 1-21
    GeneBST2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBST-2,HM1.24 ANTIGEN,TETHERIN

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit BGMSTV

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4P6Z)

(-) Sites  (0, 0)

(no "Site" information available for 4P6Z)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P6Z)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro G:2 -Ala G:3

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P6Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P6Z)

(-) Exons   (0, 0)

(no "Exon" information available for 4P6Z)

(-) 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 B from PDB  Type:PROTEIN  Length:570
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhhh.....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh.....hhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.....hhhhhhhhhhhhhhh.....hhhhhhhh........hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhh...hhhhhhh.hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4p6z B  14 EIFELKAELNSDKKEKKKEAVKKVIASMTVGKDVSALFPDVVNCMQTDNLELKKLVYLYLMNYAKSQPDMAIMAVNTFVKDCEDPNPLIRALAVRTMGCIRVDKITEYLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQLVEDQGFLDTLKDLISDSNPMVVANAVAALSEIAESHPSSNLLDLNPQSINKLLTALNECTEWGQIFILDCLANYMPKDDREAQSICERVTPRLSHANSAVVLSAVKVLMKFMEMLSKDLDYYGTLLKKLAPPLVTLLSAEPELQYVALRNINLIVQKRPEILKHEMKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAELKEYATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIKDIFRKYPNKYESVIAALCENLDSLDEPEARAAMIWIVGEYAERIDNADELLESFLEGFHDKSTQVQLQLLTAIVKLFLKKPTETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVAAKEVVLAEKPLISEETDLIEPTLLDELICYIGTLASVYHKPPSAFVE 583
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583

Chain G from PDB  Type:PROTEIN  Length:587
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......ee..eehhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p6z G   2 PAPIRLRELIRTIRTARTQAEEREMIQKECAAIRSSFREEDNTYRCRNVAKLLYMHMLGYPAHFGQLECLKLIASQKFTDKRIGYLGAMLLLDERQDVHLLMTNCIKNDLNHSTQFVQGLALCTLGCMGSSEMCRDLAGEVEKLLKTSNSYLRKKAALCAVHVIRKVPELMEMFLPATKNLLNEKNHGVLHTSVVLLTEMCERSPDMLAHFRKLVPQLVRILKNLIMSGYSPEHDVSGISDPFLQVRILRLLRILGRNDDDSSEAMNDILAQVATNTETSKNVGNAILYETVLTIMDIKSESGLRVLAINILGRFLLNNDKNIRYVALTSLLKTVQTDHNAVQRHRSTIVDCLKDLDVSIKRRAMELSFALVNGNNIRGMMKELLYFLDSCEPEFKADCASGIFLAAEKYAPSKRWHIDTIMRVLTTAGSYVRDDAVPNLIQLITNSVEMHAYTVQRLYKAILGDYSQQPLVQVAAWCIGEYGDLLVSGQCEEEEPIQVTEDEVLDILESVLISNMSTSVTRGYALTAIMKLSTRFTCTVNRIKKVVSIYGSSIDVELQQRAVEYNALFKKYDHMRSALLERMPVME 588
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       

Chain M from PDB  Type:PROTEIN  Length:415
                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....eeeeee.....hhhhhhhhhhhhhhhhhhh....eeee..eeeeeeee..eeeeeee....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhee..ee...hhhhhh..........hhhhhh..............eeeeeeeeeeeeee.....eeeeeeeeeeeeeee.....eeeeee.hhhhhhh............eeee....hhhhhhhhh.eee....eeeeeeeeeee......eeeeeeeeee...eeeeeeeeee......eeeeeeeeee.....eeeeeee...eeeeehhh.eeeeeeeeee...eeeeeeeee..............eeeeeeee........eeeeeee.......eeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p6z M   2 SASAVYVLDLKGKVLICRNYRGDVDMSEVEHFMPILMEKEEEGMLSPILAHGGVRFMWIKHNNLYLVATSKKNACVSLVFSFLYKVVQVFSEYFKELEEESIRDNFVIIYELLDELMDFGYPQTTDSKILQEYITQEAPRPPATVTNAVSWRSEGIKYRKNEVFLDVIEAVNLLVSANGNVLRSEIVGSIKMRVFLSGMPELRLGLNDKVLFDNTGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIESVIEKHSHSRIEYMVKAKSQFKRRSTANNVEIHIPVPNDADSPKFKTTVGSVKWVPENSEIVWSVKSFPGGKEYLMRAHFGLPSVEAEDKEGKPPISVKFEIPYFTTSGIQVRYLKIIEKSGYQALPWVRYITQNGDYQLRTQ 423
                                    11        21        31        41        51        61        71        81        91       101       111       121       131      |148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418     
                                                                                                                                                                  138|                                                                                                                                                                                                                                                                                     
                                                                                                                                                                   146                                                                                                                                                                                                                                                                                     

Chain S from PDB  Type:PROTEIN  Length:147
                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....eeeeee....hhhhhhhhhhhhhhhhhh.......eeee..eeeeeeee..eeeeeee....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhee..ee...hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p6z S   1 MMRFMLLFSRRGKLRLQKWYLATSDKERKKMVRELMQVVLARKPKMCSFLEWRDLKVVYKRYASLYFCCAIEGQDNELITLELIHRYVELLDKYFGSVCELDIIFNFEKAYFILDEFLMGGDVQDTSKKSVLKAIEQADLLQEEDES 147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       

Chain T from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author .....ee.... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 4p6z T   4 TSYDYCRVPME  14
                                    13 

Chain V from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author hhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4p6z V  59 DQEELSALVE  68
                                    68

   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 4P6Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P6Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P6Z)

(-) Gene Ontology  (90, 143)

Asymmetric/Biological Unit(hide GO term definitions)

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    Pro G:2 - Ala G:3   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        AP1B1_HUMAN | Q105674hmy
        AP1G1_MOUSE | P228921gyu 1gyv 1gyw 1w63 2a7b 3zy7 4hmy
        AP1M1_MOUSE | P355851w63 4emz 4en2 4hmy
        BST2_HUMAN | Q105892lk9 2x7a 2xg7 3mq7 3mq9 3mqb 3mqc 3nwh
        VPU_HV1S1 | P195541vpu 2k7y

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4P6Z)