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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHORIBOSYL DIPHOSPHATE SYNTHASE COMPLEXED WITH AMP AND RIBOSE 5-PHOSPHATE
 
Authors :  A. Kadziola, E. Johansson, C. H. Jepsen, J. Mcguire, S. Larsen, B. Hove- Jensen
Date :  11 Aug 04  (Deposition) - 23 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Prpp Synthase; Ribose 5-Phosphate; Adenosine 5'- Monophosphate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Kadziola, C. H. Jepsen, E. Johansson, J. Mcguire, S. Larsen, B. Hove-Jensen
Novel Class Iii Phosphoribosyl Diphosphate Synthase: Structure And Properties Of The Tetrameric, Phosphate-Activated, Non-Allosterically Inhibited Enzyme From Methanocaldococcus Jannaschii
J. Mol. Biol. V. 354 815 2005
PubMed-ID: 16288921  |  Reference-DOI: 10.1016/J.JMB.2005.10.001
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOSE-PHOSPHATE PYROPHOSPHOKINASE
    ChainsA, B, C, D
    EC Number2.7.6.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentPHOSPHORIBOSYL DIPHOSPHATE SYNTHASE
    GenePRS
    Organism ScientificMETHANOCALDOCOCCUS JANNASCHII
    Organism Taxid2190
    SynonymPHOSPHORIBOSYL DIPHOSPHATE SYNTHASE;
RPPK

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1AMP4Ligand/IonADENOSINE MONOPHOSPHATE
2R5P4Ligand/IonRIBOSE-5-PHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:163 , ASP A:212 , ILE A:214 , ILE A:215 , SER A:216 , THR A:217 , GLY A:218 , GLY A:219 , THR A:220 , HOH A:5445BINDING SITE FOR RESIDUE R5P A 5301
2AC2SOFTWAREASP B:163 , ASP B:212 , ILE B:214 , ILE B:215 , SER B:216 , THR B:217 , GLY B:218 , GLY B:219 , THR B:220 , HOH B:6445BINDING SITE FOR RESIDUE R5P B 6301
3AC3SOFTWAREASP C:163 , ASP C:212 , ILE C:214 , ILE C:215 , SER C:216 , THR C:217 , GLY C:218 , GLY C:219 , THR C:220 , HOH C:7445BINDING SITE FOR RESIDUE R5P C 7301
4AC4SOFTWAREASP D:163 , ASP D:212 , ILE D:214 , SER D:216 , THR D:217 , GLY D:218 , GLY D:219 , THR D:220 , HOH D:8445BINDING SITE FOR RESIDUE R5P D 8301
5AC5SOFTWAREARG A:92 , GLN A:93 , ASP A:94 , PHE A:97 , HIS A:125 , PHE B:32 , ASP B:34 , GLU B:36 , HOH B:5424 , HOH B:5437BINDING SITE FOR RESIDUE AMP B 5302
6AC6SOFTWAREPHE A:32 , ASP A:34 , GLU A:36 , ARG B:92 , GLN B:93 , ASP B:94 , PHE B:97 , HIS B:125 , HOH B:6424 , HOH B:6437BINDING SITE FOR RESIDUE AMP B 6302
7AC7SOFTWAREARG C:92 , GLN C:93 , PHE C:97 , HIS C:125 , PHE D:32 , ASP D:34 , GLU D:36 , HOH D:7424 , HOH D:7437BINDING SITE FOR RESIDUE AMP D 7302
8AC8SOFTWAREPHE C:32 , ASP C:34 , GLU C:36 , HOH C:8424 , HOH C:8437 , ARG D:92 , GLN D:93 , PHE D:97 , HIS D:125BINDING SITE FOR RESIDUE AMP C 8302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U9Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1U9Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U9Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1U9Z)

(-) Exons   (0, 0)

(no "Exon" information available for 1U9Z)

(-) 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:274
 aligned with KPRS_METJA | Q58761 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:284
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280    
           KPRS_METJA     1 MIVVSGSQSQNLAFKVAKLLNTKLTRVEYKRFPDNEIYVRIVDEINDDEAVIINTQKNQNDAIVETILLCDALRDEGVKKITLVAPYLAYARQDKKFNPGEAISIRALAKIYSNIVDKLITINPHETHIKDFFTIPFIYGDAVPKLAEYVKDKLNDPIVLAPDKGALEFAKTASKILNAEYDYLEKTRLSPTEIQIAPKTLDAKDRDVFIVDDIISTGGTMATAVKLLKEQGAKKIIAACVHPVLIGDALNKLYSAGVEEVVGTDTYLSEVSKVSVAEVIVDLL 284
               SCOP domains d1u9za1 A:1-155 Phosphoribosylpyrophosphate synthetase                                                                                                     d1u9za2 A:156-284 Phosphoribos          ylpyrophosphate synthetase                                                                SCOP domains
               CATH domains 1u9zA01 A:1-141,A:276-284  [code=3.40.50.2020, no name defined]                                                                              1u9zA02 A:142-275  [code=3.40.50.2020, no na          me defined]                                                                     1u9zA01   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhhhhhhh...ee.eeeee.....eeeee.......eeeee....hhhhhhhhhhhhhhhhhh....eeeee..................hhhhhhhhhhhhhh.eeeee...hhhhhhhh...eeee.hhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhh.eeee..----------...........eeeeeeee...hhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhh..eeee............hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u9z A   1 MIVVSGSQSQNLAFKVAKLLNTKLTRVEYKRFPDNEIYVRIVDEINDDEAVIINTQKNQNDAIVETILLCDALRDEGVKKITLVAPYLAYARQDKKFNPGEAISIRALAKIYSNIVDKLITINPHETHIKDFFTIPFIYGDAVPKLAEYVKDKLNDPIVLAPDKGALEFAKTASKILNAEYDYLE----------IAPKTLDAKDRDVFIVDDIISTGGTMATAVKLLKEQGAKKIIAACVHPVLIGDALNKLYSAGVEEVVGTDTYLSEVSKVSVAEVIVDLL 284
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    |    -     | 200       210       220       230       240       250       260       270       280    
                                                                                                                                                                                                                  185        196                                                                                        

Chain B from PDB  Type:PROTEIN  Length:274
 aligned with KPRS_METJA | Q58761 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:284
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280    
           KPRS_METJA     1 MIVVSGSQSQNLAFKVAKLLNTKLTRVEYKRFPDNEIYVRIVDEINDDEAVIINTQKNQNDAIVETILLCDALRDEGVKKITLVAPYLAYARQDKKFNPGEAISIRALAKIYSNIVDKLITINPHETHIKDFFTIPFIYGDAVPKLAEYVKDKLNDPIVLAPDKGALEFAKTASKILNAEYDYLEKTRLSPTEIQIAPKTLDAKDRDVFIVDDIISTGGTMATAVKLLKEQGAKKIIAACVHPVLIGDALNKLYSAGVEEVVGTDTYLSEVSKVSVAEVIVDLL 284
               SCOP domains d1u9zb1 B:1-155 Phosphoribosylpyrophosphate synthetase                                                                                                     d1u9zb2 B:156-284 Phosphoribos          ylpyrophosphate synthetase                                                                SCOP domains
               CATH domains 1u9zB01 B:1-141,B:276-284  [code=3.40.50.2020, no name defined]                                                                              1u9zB02 B:142-275  [code=3.40.50.2020, no na          me defined]                                                                     1u9zB01   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhhhhhhh...ee.eeeee.....eeeee.......eeeee....hhhhhhhhhhhhhhhhhh....eeeee..................hhhhhhhhhhhhhh.eeeee...hhhhhhhh...eeee.hhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhh.eeee..----------...........eeeeeeee...hhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhh..eeee............hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u9z B   1 MIVVSGSQSQNLAFKVAKLLNTKLTRVEYKRFPDNEIYVRIVDEINDDEAVIINTQKNQNDAIVETILLCDALRDEGVKKITLVAPYLAYARQDKKFNPGEAISIRALAKIYSNIVDKLITINPHETHIKDFFTIPFIYGDAVPKLAEYVKDKLNDPIVLAPDKGALEFAKTASKILNAEYDYLE----------IAPKTLDAKDRDVFIVDDIISTGGTMATAVKLLKEQGAKKIIAACVHPVLIGDALNKLYSAGVEEVVGTDTYLSEVSKVSVAEVIVDLL 284
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    |    -     | 200       210       220       230       240       250       260       270       280    
                                                                                                                                                                                                                  185        196                                                                                        

Chain C from PDB  Type:PROTEIN  Length:274
 aligned with KPRS_METJA | Q58761 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:284
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280    
           KPRS_METJA     1 MIVVSGSQSQNLAFKVAKLLNTKLTRVEYKRFPDNEIYVRIVDEINDDEAVIINTQKNQNDAIVETILLCDALRDEGVKKITLVAPYLAYARQDKKFNPGEAISIRALAKIYSNIVDKLITINPHETHIKDFFTIPFIYGDAVPKLAEYVKDKLNDPIVLAPDKGALEFAKTASKILNAEYDYLEKTRLSPTEIQIAPKTLDAKDRDVFIVDDIISTGGTMATAVKLLKEQGAKKIIAACVHPVLIGDALNKLYSAGVEEVVGTDTYLSEVSKVSVAEVIVDLL 284
               SCOP domains d1u9zc1 C:1-155 Phosphoribosylpyrophosphate synthetase                                                                                                     d1u9zc2 C:156-284 Phosphoribos          ylpyrophosphate synthetase                                                                SCOP domains
               CATH domains 1u9zC01 C:1-141,C:276-284  [code=3.40.50.2020, no name defined]                                                                              1u9zC02 C:142-275  [code=3.40.50.2020, no na          me defined]                                                                     1u9zC01   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhhhhhhh...ee.eeeee.....eeeee.......eeeee....hhhhhhhhhhhhhhhhhh....eeeee..................hhhhhhhhhhhhhh.eeeee...hhhhhhhh...eeee.hhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhh.eeee..----------...........eeeeeeee...hhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhh..eeee............hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u9z C   1 MIVVSGSQSQNLAFKVAKLLNTKLTRVEYKRFPDNEIYVRIVDEINDDEAVIINTQKNQNDAIVETILLCDALRDEGVKKITLVAPYLAYARQDKKFNPGEAISIRALAKIYSNIVDKLITINPHETHIKDFFTIPFIYGDAVPKLAEYVKDKLNDPIVLAPDKGALEFAKTASKILNAEYDYLE----------IAPKTLDAKDRDVFIVDDIISTGGTMATAVKLLKEQGAKKIIAACVHPVLIGDALNKLYSAGVEEVVGTDTYLSEVSKVSVAEVIVDLL 284
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    |    -     | 200       210       220       230       240       250       260       270       280    
                                                                                                                                                                                                                  185        196                                                                                        

Chain D from PDB  Type:PROTEIN  Length:274
 aligned with KPRS_METJA | Q58761 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:284
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280    
           KPRS_METJA     1 MIVVSGSQSQNLAFKVAKLLNTKLTRVEYKRFPDNEIYVRIVDEINDDEAVIINTQKNQNDAIVETILLCDALRDEGVKKITLVAPYLAYARQDKKFNPGEAISIRALAKIYSNIVDKLITINPHETHIKDFFTIPFIYGDAVPKLAEYVKDKLNDPIVLAPDKGALEFAKTASKILNAEYDYLEKTRLSPTEIQIAPKTLDAKDRDVFIVDDIISTGGTMATAVKLLKEQGAKKIIAACVHPVLIGDALNKLYSAGVEEVVGTDTYLSEVSKVSVAEVIVDLL 284
               SCOP domains d1u9zd1 D:1-155 Phosphoribosylpyrophosphate synthetase                                                                                                     d1u9zd2 D:156-284 Phosphoribos          ylpyrophosphate synthetase                                                                SCOP domains
               CATH domains 1u9zD01 D:1-141,D:276-284  [code=3.40.50.2020, no name defined]                                                                              1u9zD02 D:142-275  [code=3.40.50.2020, no na          me defined]                                                                     1u9zD01   CATH domains
           Pfam domains (1) Pribosyltran_N-1u9zD05 D:1-115                                                                                     -----------------Pribosyltran-1u9zD01 D:133-242                                                                                ------------------------------------------ Pfam domains (1)
           Pfam domains (2) Pribosyltran_N-1u9zD06 D:1-115                                                                                     -----------------Pribosyltran-1u9zD02 D:133-242                                                                                ------------------------------------------ Pfam domains (2)
           Pfam domains (3) Pribosyltran_N-1u9zD07 D:1-115                                                                                     -----------------Pribosyltran-1u9zD03 D:133-242                                                                                ------------------------------------------ Pfam domains (3)
           Pfam domains (4) Pribosyltran_N-1u9zD08 D:1-115                                                                                     -----------------Pribosyltran-1u9zD04 D:133-242                                                                                ------------------------------------------ Pfam domains (4)
         Sec.struct. author .eeee...hhhhhhhhhhhh...ee.eeeee.....eeeee.......eeeee....hhhhhhhhhhhhhhhhhh....eeeee..................hhhhhhhhhhhhhh.eeeee...hhhhhhhh...eeee.hhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhh.eeee..----------...........eeeeeeee...hhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhh..eeee............hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u9z D   1 MIVVSGSQSQNLAFKVAKLLNTKLTRVEYKRFPDNEIYVRIVDEINDDEAVIINTQKNQNDAIVETILLCDALRDEGVKKITLVAPYLAYARQDKKFNPGEAISIRALAKIYSNIVDKLITINPHETHIKDFFTIPFIYGDAVPKLAEYVKDKLNDPIVLAPDKGALEFAKTASKILNAEYDYLE----------IAPKTLDAKDRDVFIVDDIISTGGTMATAVKLLKEQGAKKIIAACVHPVLIGDALNKLYSAGVEEVVGTDTYLSEVSKVSVAEVIVDLL 284
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    |    -     | 200       210       220       230       240       250       260       270       280    
                                                                                                                                                                                                                  185        196                                                                                        

   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, 8)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
1a1u9zA01A:1-141,A:276-284
1b1u9zA02A:142-275
1c1u9zB02B:142-275
1d1u9zC02C:142-275
1e1u9zD02D:142-275
1f1u9zB01B:1-141,B:276-284
1g1u9zC01C:1-141,C:276-284
1h1u9zD01D:1-141,D:276-284

(-) Pfam Domains  (2, 8)

Asymmetric/Biological Unit

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (KPRS_METJA | Q58761)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0004749    ribose phosphate diphosphokinase activity    Catalysis of the reaction: D-ribose 5-phosphate + ATP = 5-phospho-alpha-D-ribose 1-diphosphate + AMP + 2 H(+).
    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.
biological process
    GO:0006015    5-phosphoribose 1-diphosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of 5-phosphoribose 1-diphosphate, also known as 5-phosphoribosyl-1-pyrophosphate.
    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:0009165    nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0009156    ribonucleoside monophosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of a ribonucleoside monophosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with phosphate on the sugar.
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
        KPRS_METJA | Q587611u9y

(-) Related Entries Specified in the PDB File

1u9y NATIVE STRUCTURE