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(-)Asym./Biol. Unit
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(-) Description

Title :  CRYSTAL STRUCTURE OF PURINE NUCLEOSIDE PHOSPHORYLASE
 
Authors :  Structural Genomix
Date :  01 Dec 03  (Deposition) - 30 Dec 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.23
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Badger, J. M. Sauder, J. M. Adams, S. Antonysamy, K. Bain, M. G. Bergseid, S. G. Buchanan, M. D. Buchanan, Y. Batiyenko, J. A. Christopher, S. Emtage, A. Eroshkina, I. Feil, E. B. Furlong, K. S. Gajiwala, X. Gao, D. He, J. Hendle, A. Huber, K. Hoda, P. Kearins, C. Kissinger, B. Laubert, H. A. Lewis, J. Lin, K. Loomis, D. Lorimer, G. Louie, M. Maletic, C. D. Marsh, I. Miller, J. Molinari, H. J. Muller-Dieckmann, J. M. Newman, B. W. Noland, B. Pagarigan, F. Park, T. S. Peat, K. W. Post, S. Radojicic, A. Ramos, R. Romero, M. E. Rutter, W. E. Sanderson, K. D. Schwinn, J. Tresser, J. Winhoven, T. A. Wright, L. Wu, J. Xu, T. J. Harris
Structural Analysis Of A Set Of Proteins Resulting From A Bacterial Genomics Project
Proteins V. 60 787 2005
PubMed-ID: 16021622  |  Reference-DOI: 10.1002/PROT.20541

(-) Compounds

Molecule 1 - PURINE NUCLEOSIDE PHOSPHORYLASE
    ChainsA, B, C, D, E, F
    EC Number2.4.2.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificVIBRIO CHOLERAE
    Organism Taxid666

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit ABCDEF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1VHJ)

(-) Sites  (0, 0)

(no "Site" information available for 1VHJ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VHJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VHJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VHJ)

(-) PROSITE Motifs  (1, 6)

Asymmetric/Biological Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PNP_UDP_1PS01232 Purine and other phosphorylases family 1 signature.DEOD1_VIBCH62-77
 
 
 
 
 
  6A:62-77
B:62-77
C:62-77
D:62-77
E:62-77
F:62-77

(-) Exons   (0, 0)

(no "Exon" information available for 1VHJ)

(-) 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:234
 aligned with DEOD1_VIBCH | Q9KPM0 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
          DEOD1_VIBCH     2 ATPHINAQMGDFADVVLMPGDPLRAKYIAENFLDNAVQVCDVRNMFGYTGTYKGRKISVMGHGMGIPSCSIYVTELIKDYGVKKIIRVGSCGAVNEGIKVRDVVIGMGACTDSKVNRIRFKDHDFAAIADYKMVKAAEEAAKARGIDVKVGNLFSAELFYTPDPSMFDVMDKYGIVGVEMEAAGIYGVAAEYGAKALAICTVSDHIKTGEQTTSEERQNTFNEMIEIALDSVLIGDQ 238
               SCOP domains d1vhja_ A: Purine nucleoside phosphorylase, PNP                                                                                                                                                                                               SCOP domains
               CATH domains 1vhjA00 A:2-238  [code=3.40.50.1580, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeee..hhhhhhhhhhhhheeeeeeehhhhh.eeeeee..eeeeee....hhhhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeeeeee..hhhhhhh.........hhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhh...eee.hhhhhhhhhhhhh.eeeeeeeeeee.....---hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------PNP_UDP_1       ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vhj A   2 ATPHINAQMGDFADVVLMPGDPLRAKYIAENFLDNAVQVCDVRNMFGYTGTYKGRRISVMGHGMGIPSCSIYVTELIKDYGVKKIIRVGSCGAVNEGIKVRDVVIGMGACTDSKVNRIRFKDHDFAAIADYKMVKAAEEAAKARGIDVKVGNLFSAELFYTPDPSMFDVMDKYGIVGVEMEAAGIYGVAAEYGAKALAICTVSDHIKTGE---SEERQNTFNEMIEIALDSVLIGDQ 238
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211   |   221       231       
                                                                                                                                                                                                                                           211 215                       

Chain B from PDB  Type:PROTEIN  Length:237
 aligned with DEOD1_VIBCH | Q9KPM0 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
          DEOD1_VIBCH     2 ATPHINAQMGDFADVVLMPGDPLRAKYIAENFLDNAVQVCDVRNMFGYTGTYKGRKISVMGHGMGIPSCSIYVTELIKDYGVKKIIRVGSCGAVNEGIKVRDVVIGMGACTDSKVNRIRFKDHDFAAIADYKMVKAAEEAAKARGIDVKVGNLFSAELFYTPDPSMFDVMDKYGIVGVEMEAAGIYGVAAEYGAKALAICTVSDHIKTGEQTTSEERQNTFNEMIEIALDSVLIGDQ 238
               SCOP domains d1vhjb_ B: Purine nucleoside phosphorylase, PNP                                                                                                                                                                                               SCOP domains
               CATH domains 1vhjB00 B:2-238  [code=3.40.50.1580, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeee..hhhhhhhhhhhh.eeeeeeehhhhh.eeeeee..eeeeee....hhhhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeeeeee..hhhhhhh......ee.hhhhhhhhhhhhhh....eeeeeeee.........hhhhhhhhh...eee.hhhhhhhhhhhhh.eeeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------PNP_UDP_1       ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vhj B   2 ATPHINAQMGDFADVVLMPGDPLRAKYIAENFLDNAVQVCDVRNMFGYTGTYKGRRISVMGHGMGIPSCSIYVTELIKDYGVKKIIRVGSCGAVNEGIKVRDVVIGMGACTDSKVNRIRFKDHDFAAIADYKMVKAAEEAAKARGIDVKVGNLFSAELFYTPDPSMFDVMDKYGIVGVEMEAAGIYGVAAEYGAKALAICTVSDHIKTGEQTTSEERQNTFNEMIEIALDSVLIGDQ 238
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       

Chain C from PDB  Type:PROTEIN  Length:232
 aligned with DEOD1_VIBCH | Q9KPM0 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
          DEOD1_VIBCH     2 ATPHINAQMGDFADVVLMPGDPLRAKYIAENFLDNAVQVCDVRNMFGYTGTYKGRKISVMGHGMGIPSCSIYVTELIKDYGVKKIIRVGSCGAVNEGIKVRDVVIGMGACTDSKVNRIRFKDHDFAAIADYKMVKAAEEAAKARGIDVKVGNLFSAELFYTPDPSMFDVMDKYGIVGVEMEAAGIYGVAAEYGAKALAICTVSDHIKTGEQTTSEERQNTFNEMIEIALDSVLIGDQ 238
               SCOP domains d1vhjc_ C: Purine nucleoside phosphorylase, PNP                                                                                                                                                                                               SCOP domains
               CATH domains 1vhjC00 C:2-238  [code=3.40.50.1580, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeee..hhhhhhhhhhhhheeeeeeehhhhh.eeeeee..eeeeee....hhhhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeeeeee..hhhhhhh......ee.hhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhh...eee.hhhhhhhhhhhh..eeeeeeeeeee.....-----hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------PNP_UDP_1       ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vhj C   2 ATPHINAQMGDFADVVLMPGDPLRAKYIAENFLDNAVQVCDVRNMFGYTGTYKGRRISVMGHGMGIPSCSIYVTELIKDYGVKKIIRVGSCGAVNEGIKVRDVVIGMGACTDSKVNRIRFKDHDFAAIADYKMVKAAEEAAKARGIDVKVGNLFSAELFYTPDPSMFDVMDKYGIVGVEMEAAGIYGVAAEYGAKALAICTVSDHIKTGE-----ERQNTFNEMIEIALDSVLIGDQ 238
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     | 221       231       
                                                                                                                                                                                                                                           211   217                     

Chain D from PDB  Type:PROTEIN  Length:232
 aligned with DEOD1_VIBCH | Q9KPM0 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
          DEOD1_VIBCH     2 ATPHINAQMGDFADVVLMPGDPLRAKYIAENFLDNAVQVCDVRNMFGYTGTYKGRKISVMGHGMGIPSCSIYVTELIKDYGVKKIIRVGSCGAVNEGIKVRDVVIGMGACTDSKVNRIRFKDHDFAAIADYKMVKAAEEAAKARGIDVKVGNLFSAELFYTPDPSMFDVMDKYGIVGVEMEAAGIYGVAAEYGAKALAICTVSDHIKTGEQTTSEERQNTFNEMIEIALDSVLIGDQ 238
               SCOP domains d1vhjd_ D: Purine nucleoside phosphorylase, PNP                                                                                                                                                                                               SCOP domains
               CATH domains 1vhjD00 D:2-238  [code=3.40.50.1580, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeee..hhhhhhhhhhhhheeeeeeehhhhh.eeeeee..eeeeee....hhhhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeeeeee..hhhhhhh......ee.hhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhh...eee.hhhhhhhhhhhh..eeeeeeeeeee.....-----hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------PNP_UDP_1       ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vhj D   2 ATPHINAQMGDFADVVLMPGDPLRAKYIAENFLDNAVQVCDVRNMFGYTGTYKGRRISVMGHGMGIPSCSIYVTELIKDYGVKKIIRVGSCGAVNEGIKVRDVVIGMGACTDSKVNRIRFKDHDFAAIADYKMVKAAEEAAKARGIDVKVGNLFSAELFYTPDPSMFDVMDKYGIVGVEMEAAGIYGVAAEYGAKALAICTVSDHIKTGE-----ERQNTFNEMIEIALDSVLIGDQ 238
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     | 221       231       
                                                                                                                                                                                                                                           211   217                     

Chain E from PDB  Type:PROTEIN  Length:232
 aligned with DEOD1_VIBCH | Q9KPM0 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
          DEOD1_VIBCH     2 ATPHINAQMGDFADVVLMPGDPLRAKYIAENFLDNAVQVCDVRNMFGYTGTYKGRKISVMGHGMGIPSCSIYVTELIKDYGVKKIIRVGSCGAVNEGIKVRDVVIGMGACTDSKVNRIRFKDHDFAAIADYKMVKAAEEAAKARGIDVKVGNLFSAELFYTPDPSMFDVMDKYGIVGVEMEAAGIYGVAAEYGAKALAICTVSDHIKTGEQTTSEERQNTFNEMIEIALDSVLIGDQ 238
               SCOP domains d1vhje_ E: Purine nucleoside phosphorylase, PNP                                                                                                                                                                                               SCOP domains
               CATH domains 1vhjE00 E:2-238  [code=3.40.50.1580, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeee..hhhhhhhhhhhhheeeeeeehhhhh.eeeeee..eeeeee....hhhhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeeeeee..hhhhhhh......ee.hhhhhhhhhhhhhh....eeeeeeee.........hhhhhhhhh...eee.hhhhhhhhhhhhh.eeeeeeeeeee.....-----hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------PNP_UDP_1       ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vhj E   2 ATPHINAQMGDFADVVLMPGDPLRAKYIAENFLDNAVQVCDVRNMFGYTGTYKGRRISVMGHGMGIPSCSIYVTELIKDYGVKKIIRVGSCGAVNEGIKVRDVVIGMGACTDSKVNRIRFKDHDFAAIADYKMVKAAEEAAKARGIDVKVGNLFSAELFYTPDPSMFDVMDKYGIVGVEMEAAGIYGVAAEYGAKALAICTVSDHIKTGE-----ERQNTFNEMIEIALDSVLIGDQ 238
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     | 221       231       
                                                                                                                                                                                                                                           211   217                     

Chain F from PDB  Type:PROTEIN  Length:237
 aligned with DEOD1_VIBCH | Q9KPM0 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
          DEOD1_VIBCH     2 ATPHINAQMGDFADVVLMPGDPLRAKYIAENFLDNAVQVCDVRNMFGYTGTYKGRKISVMGHGMGIPSCSIYVTELIKDYGVKKIIRVGSCGAVNEGIKVRDVVIGMGACTDSKVNRIRFKDHDFAAIADYKMVKAAEEAAKARGIDVKVGNLFSAELFYTPDPSMFDVMDKYGIVGVEMEAAGIYGVAAEYGAKALAICTVSDHIKTGEQTTSEERQNTFNEMIEIALDSVLIGDQ 238
               SCOP domains d1vhjf_ F: Purine nucleoside phosphorylase, PNP                                                                                                                                                                                               SCOP domains
               CATH domains 1vhjF00 F:2-238  [code=3.40.50.1580, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeee..hhhhhhhhhhhh.eeeeeeehhhhh.eeeeee..eeeeee....hhhhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeeeeee..hhhhhhh......ee.hhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhh...eee.hhhhhhhhhhhh..eeeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------PNP_UDP_1       ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vhj F   2 ATPHINAQMGDFADVVLMPGDPLRAKYIAENFLDNAVQVCDVRNMFGYTGTYKGRRISVMGHGMGIPSCSIYVTELIKDYGVKKIIRVGSCGAVNEGIKVRDVVIGMGACTDSKVNRIRFKDHDFAAIADYKMVKAAEEAAKARGIDVKVGNLFSAELFYTPDPSMFDVMDKYGIVGVEMEAAGIYGVAAEYGAKALAICTVSDHIKTGEQTTSEERQNTFNEMIEIALDSVLIGDQ 238
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       

   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  (1, 6)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1VHJ)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (DEOD1_VIBCH | Q9KPM0)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004731    purine-nucleoside phosphorylase activity    Catalysis of the reaction: purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
    GO:0016763    transferase activity, transferring pentosyl groups    Catalysis of the transfer of a pentosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
    GO:0009116    nucleoside metabolic process    The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
    GO:0042278    purine nucleoside metabolic process    The chemical reactions and pathways involving one of a family of organic molecules consisting of a purine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).

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 Related Entries

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

UniProtKB/Swiss-Prot
        DEOD1_VIBCH | Q9KPM01vhw 3of3

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1VHJ)