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(-) Description

Title :  HIGH RESOLUTION HIV-2 PROTEASE STRUCTURE IN COMPLEX WITH CLINICAL DRUG DARUNAVIR
 
Authors :  A. Y. Kovalevsky, I. T. Weber
Date :  28 Aug 08  (Deposition) - 16 Sep 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hiv-2, Aspartic Protease, Inhibitor, Protease-Drug Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Y. Kovalevsky, J. M. Louis, A. Aniana, A. K. Ghosh, I. T. Weber
Structural Evidence For Effectiveness Of Darunavir And Two Related Antiviral Inhibitors Against Hiv-2 Protease
J. Mol. Biol. V. 384 178 2008
PubMed-ID: 18834890  |  Reference-DOI: 10.1016/J.JMB.2008.09.031

(-) Compounds

Molecule 1 - PROTEASE
    ChainsA, B
    EC Number3.4.23.47
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET11A
    Expression System StrainBL21 (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificHUMAN IMMUNODEFICIENCY VIRUS TYPE 2 (ISOLATE ROD)
    Organism Taxid11720

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 25)

Asymmetric/Biological Unit (5, 25)
No.NameCountTypeFull Name
10171Ligand/Ion(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE
2CL8Ligand/IonCHLORIDE ION
3IMD6Ligand/IonIMIDAZOLE
4NA1Ligand/IonSODIUM ION
5ZN9Ligand/IonZINC ION

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:2 , PHE A:3 , LEU A:99 , ZN A:403 , CL A:503 , HOH A:1011 , HOH A:1148BINDING SITE FOR RESIDUE IMD A 304
02AC2SOFTWARETYR A:14 , GLY A:17 , GLU A:63 , GLU A:65 , ZN A:406BINDING SITE FOR RESIDUE IMD A 306
03AC3SOFTWARELYS A:7 , LEU A:99 , IMD A:304 , CL A:503 , HOH A:1009 , HOH A:1010 , HOH A:1011BINDING SITE FOR RESIDUE ZN A 403
04AC4SOFTWAREASP A:79 , HOH A:1029 , HOH A:1030 , GLU B:137BINDING SITE FOR RESIDUE ZN A 405
05AC5SOFTWAREGLU A:65 , IMD A:306 , HOH A:1007BINDING SITE FOR RESIDUE ZN A 406
06AC6SOFTWARESER A:4 , LEU A:99 , IMD A:304 , ZN A:403 , HOH A:1010 , HOH A:1011 , HOH A:1105BINDING SITE FOR RESIDUE CL A 503
07AC7SOFTWAREASN A:40 , ASN A:41 , PRO A:44 , HOH A:1067 , HOH A:1090 , HOH A:1109 , ASN B:140BINDING SITE FOR RESIDUE NA A 601
08AC8SOFTWAREASP A:25 , GLY A:27 , ALA A:28 , ASP A:30 , ILE A:32 , GLY A:48 , GLY A:49 , ILE A:82 , ILE A:84 , ASP B:125 , GLY B:127 , ALA B:128 , ASP B:129 , ASP B:130 , GLY B:148 , GLY B:149 , ILE B:150 , HOH B:1017BINDING SITE FOR RESIDUE 017 B 201
09AC9SOFTWAREGLU B:121 , ILE B:146 , PHE B:153 , ASN B:155 , ASP B:179 , IMD B:302 , ZN B:401BINDING SITE FOR RESIDUE IMD B 301
10BC1SOFTWAREGLU B:121 , PHE B:153 , ASP B:179 , IMD B:301 , ZN B:401 , HOH B:1153BINDING SITE FOR RESIDUE IMD B 302
11BC2SOFTWAREASP B:130 , ILE B:146 , MET B:176 , ZN B:402 , ZN B:409 , CL B:501 , CL B:502 , CL B:507BINDING SITE FOR RESIDUE IMD B 303
12BC3SOFTWAREARG A:8 , PRO A:81 , TRP B:106 , ZN B:404 , CL B:505 , CL B:506 , HOH B:1061BINDING SITE FOR RESIDUE IMD B 305
13BC4SOFTWAREGLU B:121 , ASP B:179 , IMD B:301 , IMD B:302BINDING SITE FOR RESIDUE ZN B 401
14BC5SOFTWAREASP B:130 , IMD B:303 , ZN B:409 , CL B:502 , HOH B:1002BINDING SITE FOR RESIDUE ZN B 402
15BC6SOFTWAREIMD B:305 , CL B:505 , CL B:506 , HOH B:1004 , HOH B:1006BINDING SITE FOR RESIDUE ZN B 404
16BC7SOFTWAREGLU B:165 , CL B:504 , HOH B:1003 , HOH B:1005 , HOH B:1008BINDING SITE FOR RESIDUE ZN B 407
17BC8SOFTWAREGLU B:158 , CL B:507 , HOH B:1001 , HOH B:1170BINDING SITE FOR RESIDUE ZN B 408
18BC9SOFTWAREASP B:130 , IMD B:303 , ZN B:402 , CL B:508 , HOH B:1002BINDING SITE FOR RESIDUE ZN B 409
19CC1SOFTWAREVAL B:111 , THR B:112 , LYS B:145 , ILE B:146 , IMD B:303 , HOH B:1050BINDING SITE FOR RESIDUE CL B 501
20CC2SOFTWARELYS B:107 , GLY B:148 , IMD B:303 , ZN B:402BINDING SITE FOR RESIDUE CL B 502
21CC3SOFTWAREGLY A:39 , GLY B:117 , ZN B:407BINDING SITE FOR RESIDUE CL B 504
22CC4SOFTWARESER B:104 , LEU B:105 , TRP B:106 , LYS B:107 , IMD B:305 , ZN B:404BINDING SITE FOR RESIDUE CL B 505
23CC5SOFTWAREIMD B:305 , ZN B:404 , HOH B:1006 , HOH B:1112BINDING SITE FOR RESIDUE CL B 506
24CC6SOFTWARELYS B:145 , GLU B:158 , IMD B:303 , ZN B:408 , HOH B:1133BINDING SITE FOR RESIDUE CL B 507
25CC7SOFTWAREASP B:130 , ZN B:409 , HOH B:1002BINDING SITE FOR RESIDUE CL B 508

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EBZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3EBZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EBZ)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ASP_PROT_RETROVPS50175 Aspartyl protease, retroviral-type family profile.POL_HV2RO533-602
 
  2A:20-89
B:120-189
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.POL_HV2RO535-546
 
  2A:22-33
B:122-133

(-) Exons   (0, 0)

(no "Exon" information available for 3EBZ)

(-) 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:99
 aligned with POL_HV2RO | P04584 from UniProtKB/Swiss-Prot  Length:1464

    Alignment length:99
                                   523       533       543       553       563       573       583       593       603         
            POL_HV2RO   514 PQFSLWKRPVVTAYIEGQPVEVLLDTGADDSIVAGIELGNNYSPKIVGGIGGFINTKEYKNVEIEVLNKKVRATIMTGDTPINIFGRNILTALGMSLNL 612
               SCOP domains d3ebza_ A: Human immunodeficiency virus type 2 (HIV-2) protease                                     SCOP domains
               CATH domains 3ebzA00 A:1-99 Acid Proteases                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeeee.....eehhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------ASP_PROT_RETROV  PDB: A:20-89 UniProt: 533-602                        ---------- PROSITE (1)
                PROSITE (2) ---------------------ASP_PROTEASE------------------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 3ebz A   1 PQFSLWKRPVVTAYIEGQPVEVLLDTGADDSIVAGIELGNNYSPKIVGGIGGFINTKEYKNVEIEVLNKKVRATIMTGDTPINIFGRNILTALGMSLNL  99
                                    10        20        30        40        50        60        70        80        90         

Chain B from PDB  Type:PROTEIN  Length:99
 aligned with POL_HV2RO | P04584 from UniProtKB/Swiss-Prot  Length:1464

    Alignment length:99
                                   523       533       543       553       563       573       583       593       603         
            POL_HV2RO   514 PQFSLWKRPVVTAYIEGQPVEVLLDTGADDSIVAGIELGNNYSPKIVGGIGGFINTKEYKNVEIEVLNKKVRATIMTGDTPINIFGRNILTALGMSLNL 612
               SCOP domains d3ebzb_ B: Human immunodeficiency virus type 2 (HIV-2) protease                                     SCOP domains
               CATH domains 3ebzB00 B:101-199 Acid Proteases                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------ASP_PROT_RETROV  PDB: B:120-189 UniProt: 533-602                      ---------- PROSITE (1)
                PROSITE (2) ---------------------ASP_PROTEASE------------------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 3ebz B 101 PQFSLWKRPVVTAYIEGQPVEVLLDTGADDSIVAGIELGNNYSPKIVGGIGGFINTKEYKNVEIEVLNKKVRATIMTGDTPINIFGRNILTALGMSLNL 199
                                   110       120       130       140       150       160       170       180       190         

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EBZ)

(-) Gene Ontology  (44, 44)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (POL_HV2RO | P04584)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004523    RNA-DNA hybrid ribonuclease activity    Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
    GO:0003964    RNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    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:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0004533    exoribonuclease H activity    Catalysis of the exonucleolytic cleavage of RNA to 5'-phosphomonoester oligonucleotides in both 5' to 3' and 3' to 5' directions.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0015074    DNA integration    The process in which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome.
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0090503    RNA phosphodiester bond hydrolysis, exonucleolytic    The chemical reactions and pathways involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0006278    RNA-dependent DNA biosynthetic process    A DNA biosynthetic process that uses RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strand.
    GO:0075713    establishment of integrated proviral latency    A process by which the virus integrates into the host genome and establishes as a stable provirus or prophage.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0039657    suppression by virus of host gene expression    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of gene expression in the host organism. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0075732    viral penetration into host nucleus    The crossing by the virus of the host nuclear membrane, either as naked viral genome or for small viruses as an intact capsid.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019076    viral release from host cell    The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0044174    host cell endosome    A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to host cell lysosomes for degradation.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    GO:0072494    host multivesicular body    A late endosome in which regions of the limiting host cell endosomal membrane invaginate to form internal vesicles; host membrane proteins that enter the internal vesicles are sequestered from the host cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019013    viral nucleocapsid    The complete protein-nucleic acid complex that is the packaged form of the genome in a virus particle.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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 Related Entries

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

UniProtKB/Swiss-Prot
        POL_HV2RO | P045841e0e 1hii 1hsh 1hsi 1ida 1idb 1ivp 1ivq 1jld 1mu2 1phv 2hpe 2hpf 2k4e 2k4h 2k4i 2mip 2phv 3ec0 3ecg 3f9k 3upj 4upj 5upj 6upj

(-) Related Entries Specified in the PDB File

3ec0