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(-) Description

Title :  ESCHERICHIA COLI PURINE NUCLEOSIDE PHOSPHORYLASE II, THE PRODUCT OF THE XAPA GENE
 
Authors :  G. Dandanell, R. H. Szczepanowski, B. Kierdaszuk, D. Shugar, M. Bochtl
Date :  02 Feb 05  (Deposition) - 19 Apr 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Biol. Unit 2:  A,B,C  (1x)
Keywords :  Purine Nucleoside Phosphorylase, Guanine, Xanthine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Dandanell, R. H. Szczepanowski, B. Kierdaszuk, D. Shugar, M. Bochtler
Escherichia Coli Purine Nucleoside Phosphorylase Ii, The Product Of The Xapa Gene
J. Mol. Biol. V. 348 113 2005
PubMed-ID: 15808857  |  Reference-DOI: 10.1016/J.JMB.2005.02.019

(-) Compounds

Molecule 1 - XANTHOSINE PHOSPHORYLASE
    ChainsA, B, C
    EC Number2.4.2.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGD265
    Expression System StrainGD1524
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneXAPA
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymPNP-II, PURINE NUCLEOSIDE PHOSPHORYLASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (2x)ABC
Biological Unit 2 (1x)ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1GUN3Ligand/IonGUANINE
2PO43Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1GUN6Ligand/IonGUANINE
2PO46Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1GUN3Ligand/IonGUANINE
2PO43Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:34 , HIS A:65 , ARG A:85 , HIS A:87 , ASN A:116 , ALA A:117 , SER A:216BINDING SITE FOR RESIDUE PO4 A 500
2AC2SOFTWARESER B:34 , HIS B:65 , ARG B:85 , HIS B:87 , ASN B:116 , ALA B:117 , SER B:216 , HOH B:1532 , HOH B:1535 , HOH B:1560BINDING SITE FOR RESIDUE PO4 B 1500
3AC3SOFTWARESER C:34 , HIS C:65 , ARG C:85 , HIS C:87 , ASN C:116 , ALA C:117 , SER C:216BINDING SITE FOR RESIDUE PO4 C 2500
4AC4SOFTWAREALA A:117 , ALA A:118 , GLY A:119 , GLU A:197 , GLY A:214 , MET A:215 , THR A:238 , ASN A:239 , THR A:254 , HOH A:523BINDING SITE FOR RESIDUE GUN A 400
5AC5SOFTWAREALA B:117 , ALA B:118 , GLY B:119 , GLU B:197 , GLY B:214 , MET B:215 , THR B:238 , ASN B:239 , THR B:254 , HOH B:1560BINDING SITE FOR RESIDUE GUN B 1400
6AC6SOFTWAREALA C:117 , ALA C:118 , GLY C:119 , GLU C:197 , GLY C:214 , MET C:215 , THR C:238 , ASN C:239 , THR C:254 , HOH C:2518 , HOH C:2527 , HOH C:2553BINDING SITE FOR RESIDUE GUN C 2400

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:193 -Pro A:194
2Gly B:193 -Pro B:194
3Gly C:193 -Pro C:194

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PNP_MTAP_2PS01240 Purine and other phosphorylases family 2 signature.XAPA_ECOLI80-121
 
 
  3A:80-121
B:80-121
C:80-121
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PNP_MTAP_2PS01240 Purine and other phosphorylases family 2 signature.XAPA_ECOLI80-121
 
 
  6A:80-121
B:80-121
C:80-121
Biological Unit 2 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PNP_MTAP_2PS01240 Purine and other phosphorylases family 2 signature.XAPA_ECOLI80-121
 
 
  3A:80-121
B:80-121
C:80-121

(-) Exons   (0, 0)

(no "Exon" information available for 1YQQ)

(-) Sequences/Alignments

Asymmetric 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:273
 aligned with XAPA_ECOLI | P45563 from UniProtKB/Swiss-Prot  Length:277

    Alignment length:273
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274   
           XAPA_ECOLI     5 QFSHNPLFCIDIIKTYKPDFTPRVAFILGSGLGALADQIENAVAISYEKLPGFPVSTVHGHAGELVLGHLQGVPVVCMKGRGHFYEGRGMTIMTDAIRTFKLLGCELLFCTNAAGSLRPEVGAGSLVALKDHINTMPGTPMVGLNDDRFGERFFSLANAYDAEYRALLQKVAKEEGFPLTEGVFVSYPGPNFETAAEIRMMQIIGGDVVGMSVVPEVISARHCDLKVVAVSAITNMAEGLSDVKLSHAQTLAAAELSKQNFINLICGFLRKIA 277
               SCOP domains d1yqqa_ A: automated matches                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1yqqA00 A:5-277  [code=3.40.50.1580, no name defined]                                                                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh......eeeee..hhhhhhhhheeeeeee.hhh.............eeeeeee..eeeeeee...hhhhh.....hhhhhhhhhhhh..eeeeeeeeee.........eeeeeeee...........................hhhhhhhhhhhhhh....eeeeeeee.......hhhhhhhhhhh...eee..hhhhhhhhhhh..eeeeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------PNP_MTAP_2  PDB: A:80-121 UniProt: 80-121 ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yqq A   5 QFSHNPLFCIDIIKTYKPDFTPRVAFILGSGLGALADQIENAVAISYEKLPGFPVSTVHGHAGELVLGHLQGVPVVCMKGRGHFYEGRGMTIMTDAIRTFKLLGCELLFCTNAAGSLRPEVGAGSLVALKDHINTMPGTPMVGLNDDRFGERFFSLANAYDAEYRALLQKVAKEEGFPLTEGVFVSYPGPNFETAAEIRMMQIIGGDVVGMSVVPEVISARHCDLKVVAVSAITNMAEGLSDVKLSHAQTLAAAELSKQNFINLICGFLRKIA 277
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274   

Chain B from PDB  Type:PROTEIN  Length:273
 aligned with XAPA_ECOLI | P45563 from UniProtKB/Swiss-Prot  Length:277

    Alignment length:273
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274   
           XAPA_ECOLI     5 QFSHNPLFCIDIIKTYKPDFTPRVAFILGSGLGALADQIENAVAISYEKLPGFPVSTVHGHAGELVLGHLQGVPVVCMKGRGHFYEGRGMTIMTDAIRTFKLLGCELLFCTNAAGSLRPEVGAGSLVALKDHINTMPGTPMVGLNDDRFGERFFSLANAYDAEYRALLQKVAKEEGFPLTEGVFVSYPGPNFETAAEIRMMQIIGGDVVGMSVVPEVISARHCDLKVVAVSAITNMAEGLSDVKLSHAQTLAAAELSKQNFINLICGFLRKIA 277
               SCOP domains d1yqqb_ B: automated matches                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1yqqB00 B:5-277  [code=3.40.50.1580, no name defined]                                                                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh......eeeee..hhhhhhhhheeeeeee.hhh.............eeeeee....eeeeee...hhhhh.....hhhhhhhhhhhh..eeeeeeeeee.........eeeeeeee...........................hhhhhhhhhhhhhh.....eeeeeee.......hhhhhhhhhhh...eee..hhhhhhhhhhh..eeeeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------PNP_MTAP_2  PDB: B:80-121 UniProt: 80-121 ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yqq B   5 QFSHNPLFCIDIIKTYKPDFTPRVAFILGSGLGALADQIENAVAISYEKLPGFPVSTVHGHAGELVLGHLQGVPVVCMKGRGHFYEGRGMTIMTDAIRTFKLLGCELLFCTNAAGSLRPEVGAGSLVALKDHINTMPGTPMVGLNDDRFGERFFSLANAYDAEYRALLQKVAKEEGFPLTEGVFVSYPGPNFETAAEIRMMQIIGGDVVGMSVVPEVISARHCDLKVVAVSAITNMAEGLSDVKLSHAQTLAAAELSKQNFINLICGFLRKIA 277
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274   

Chain C from PDB  Type:PROTEIN  Length:273
 aligned with XAPA_ECOLI | P45563 from UniProtKB/Swiss-Prot  Length:277

    Alignment length:273
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274   
           XAPA_ECOLI     5 QFSHNPLFCIDIIKTYKPDFTPRVAFILGSGLGALADQIENAVAISYEKLPGFPVSTVHGHAGELVLGHLQGVPVVCMKGRGHFYEGRGMTIMTDAIRTFKLLGCELLFCTNAAGSLRPEVGAGSLVALKDHINTMPGTPMVGLNDDRFGERFFSLANAYDAEYRALLQKVAKEEGFPLTEGVFVSYPGPNFETAAEIRMMQIIGGDVVGMSVVPEVISARHCDLKVVAVSAITNMAEGLSDVKLSHAQTLAAAELSKQNFINLICGFLRKIA 277
               SCOP domains d1yqqc_ C: automated matches                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1yqqC00 C:5-277  [code=3.40.50.1580, no name defined]                                                                                                                                                                                                                             CATH domains
           Pfam domains (1) ----------------------PNP_UDP_1-1yqqC01 C:27-274                                                                                                                                                                                                                              --- Pfam domains (1)
           Pfam domains (2) ----------------------PNP_UDP_1-1yqqC02 C:27-274                                                                                                                                                                                                                              --- Pfam domains (2)
           Pfam domains (3) ----------------------PNP_UDP_1-1yqqC03 C:27-274                                                                                                                                                                                                                              --- Pfam domains (3)
         Sec.struct. author ...hhhhhhhhhhhhhh......eeeee..hhhhhhhhheeeeeee.hhh.............eeeeeee..eeeeeee...hhhhh.....hhhhhhhhhhhh..eeeeeeeeee.........eeeeeeee...........................hhhhhhhhhhhhhh....eeeeeeee.......hhhhhhhhhhh...eee..hhhhhhhhhhh..eeeeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------PNP_MTAP_2  PDB: C:80-121 UniProt: 80-121 ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yqq C   5 QFSHNPLFCIDIIKTYKPDFTPRVAFILGSGLGALADQIENAVAISYEKLPGFPVSTVHGHAGELVLGHLQGVPVVCMKGRGHFYEGRGMTIMTDAIRTFKLLGCELLFCTNAAGSLRPEVGAGSLVALKDHINTMPGTPMVGLNDDRFGERFFSLANAYDAEYRALLQKVAKEEGFPLTEGVFVSYPGPNFETAAEIRMMQIIGGDVVGMSVVPEVISARHCDLKVVAVSAITNMAEGLSDVKLSHAQTLAAAELSKQNFINLICGFLRKIA 277
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274   

   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, 3)

Asymmetric Unit

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: PUP (121)

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (XAPA_ECOLI | P45563)
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:0047975    guanosine phosphorylase activity    Catalysis of the reaction: guanosine + phosphate = guanine + D-ribose 1-phosphate.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0047724    inosine nucleosidase activity    Catalysis of the reaction: inosine + H2O = D-ribose + hypoxanthine.
    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:0006161    deoxyguanosine catabolic process    The chemical reactions and pathways resulting in the breakdown of deoxyguanosine, a nucleoside consisting of the base guanine and the sugar deoxyribose.
    GO:0006149    deoxyinosine catabolic process    The chemical reactions and pathways resulting in the breakdown of deoxyinosine, hypoxanthine deoxyriboside.
    GO:0046115    guanosine catabolic process    The chemical reactions and pathways resulting in the breakdown of guanine, guanine riboside, a nucleoside with a wide species distribution.
    GO:0006148    inosine catabolic process    The chemical reactions and pathways resulting in the breakdown of inosine, hypoxanthine riboside, a nucleoside found free but not in combination in nucleic acids except in the anticodons of some tRNAs.
    GO:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
    GO:0015949    nucleobase-containing small molecule interconversion    The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
    GO:0055086    nucleobase-containing small molecule metabolic process    The cellular chemical reactions and pathways involving a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide.
    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:0034214    protein hexamerization    The formation of a protein hexamer, a macromolecular structure consisting of six noncovalently associated identical or nonidentical subunits.
    GO:0006152    purine nucleoside catabolic process    The chemical reactions and pathways resulting in the breakdown of purine nucleoside, one of a family of organic molecules consisting of a purine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
    GO:0043101    purine-containing compound salvage    Any process that generates a purine-containing compound, any nucleobase, nucleoside, nucleotide or nucleic acid that contains a purine base, from derivatives of them without de novo synthesis.
    GO:1903228    xanthosine catabolic process    The chemical reactions and pathways resulting in the breakdown of xanthosine.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        XAPA_ECOLI | P455631yqu 1yr3

(-) Related Entries Specified in the PDB File

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