Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
(-)Biological Unit 5
(-)Biological Unit 6
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)
Image Biological Unit 5
Biological Unit 5  (Jmol Viewer)
Image Biological Unit 6
Biological Unit 6  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF 4-DEOXY-1-THREO-5-HEXOSULOSE-URONATE KETOL-ISOMERASE FROM ENTEROCOCCUS FAECALIS
 
Authors :  A. A. Fedorov, E. V. Fedorov, S. C. Almo, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  18 Feb 05  (Deposition) - 01 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Keywords :  Structural Genomics, Nysgxrc Target T1814, Ketol-Isomerase, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Fedorov, E. V. Fedorov, S. C. Almo
Crystal Structure Of 4-Deoxy-1-Threo-5-Hexosulose-Uronate Ketol-Isomerase From Enterococcus Faecalis V583
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 4-DEOXY-L-THREO-5-HEXOSULOSE-URONATE KETOL- ISOMERASE 1
    Chains: A, B, C, D, E, F
    EC Number: 5.3.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: KDUI1, KDUI-1
    Organism Scientific: ENTEROCOCCUS FAECALIS
    Organism Taxid: 1351
    Synonym: 5-KETO-4-DEOXYURONATE ISOMERASE 1, DKI ISOMERASE 1

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A     
Biological Unit 2 (1x):  B    
Biological Unit 3 (1x):   C   
Biological Unit 4 (1x):    D  
Biological Unit 5 (1x):     E 
Biological Unit 6 (1x):      F

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1YWK)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YWK)

(-) 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:255
 aligned with KDUI1_ENTFA | Q838L9 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:263
                               1                                                                                                                                                                                                                                                                   
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257   
         KDUI1_ENTFA      - ---METRYTHSPADIRHYSTEQLRDEFLVEKVFIPGAISLTYTHNDRMIFGGVTPTTEELEIILDKELGVDYFLERRELGVINIGGPGFIEIDGAKETMKKQDGYYIGKETKHVRFSSENPDNPAKFYISCVPAHHKYPNVKISIDEITPMETGDPLTLNQRKIYQYIHPNVCESCQLQMGYTILEPGSAWNTMPCHTHERRMEAYVYFDMEEDTRIFHMMGKPDETKHLVMSNEQAAISPSWSIHSGVGTSNYSFIWAMCGE  260
               SCOP domains ---d1ywka1 A:1001-1260 5-keto-4-deoxyuronate isomerase KduI                                                                                                                                                                                                             SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhh..hhhhhhhhhee........eeeeee....eeeeee......ee...hhhhh.......eeeeeee....eeeee..eeeee....eeee......eeeee........eeeeeee.......eee...........hhhhh..eeeeeee..........eeeeeee........--------.eeeeeee.......eeeee......eeeee...eeeee.......eee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ywk A  998 LQNMETRYTHSPADIRHYSTEQLRDEFLVEKVFIPGAISLTYTHNDRMIFGGVTPTTEELEIILDKELGVDYFLERRELGVINIGGPGFIEIDGAKETMKKQDGYYIGKETKHVRFSSENPDNPAKFYISCVPAHHKYPNVKISIDEITPMETGDPLTLNQRKIYQYIHPNVCESCQLQMGYTILEPGSAWNT--------RMEAYVYFDMEEDTRIFHMMGKPDETKHLVMSNEQAAISPSWSIHSGVGTSNYSFIWAMCGE 1260
                                  1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      1147      1157      1167      1177      1187  |      - |    1207      1217      1227      1237      1247      1257   
                                                                                                                                                                                                                         1190     1199                                                             


Chain B from PDB  Type:PROTEIN  Length:254
 aligned with KDUI1_ENTFA | Q838L9 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:263
                               1                                                                                                                                                                                                                                                                   
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257   
         KDUI1_ENTFA      - ---METRYTHSPADIRHYSTEQLRDEFLVEKVFIPGAISLTYTHNDRMIFGGVTPTTEELEIILDKELGVDYFLERRELGVINIGGPGFIEIDGAKETMKKQDGYYIGKETKHVRFSSENPDNPAKFYISCVPAHHKYPNVKISIDEITPMETGDPLTLNQRKIYQYIHPNVCESCQLQMGYTILEPGSAWNTMPCHTHERRMEAYVYFDMEEDTRIFHMMGKPDETKHLVMSNEQAAISPSWSIHSGVGTSNYSFIWAMCGE  260
               SCOP domains d1ywkb_ B: 5-keto-4-deoxyuronate isomerase KduI                                                                                                                                                                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...........hhhhhhhhhee........eeeeee....eeeeee......ee...hhhhh.......eeeeeee....eeeee..eeeee....eeee......eeeee........eeeeeee.......eee...........hhhhh..eeeeeee..........eeeeeee........---------.eeeeee.......eeeee......eeeee...eeeee.......eee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ywk B  998 LQNMETRYTHSPADIRHYSTEQLRDEFLVEKVFIPGAISLTYTHNDRMIFGGVTPTTEELEIILDKELGVDYFLERRELGVINIGGPGFIEIDGAKETMKKQDGYYIGKETKHVRFSSENPDNPAKFYISCVPAHHKYPNVKISIDEITPMETGDPLTLNQRKIYQYIHPNVCESCQLQMGYTILEPGSAWNT---------MEAYVYFDMEEDTRIFHMMGKPDETKHLVMSNEQAAISPSWSIHSGVGTSNYSFIWAMCGE 1260
                                  1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      1147      1157      1167      1177      1187  |      -  |   1207      1217      1227      1237      1247      1257   
                                                                                                                                                                                                                         1190      1200                                                            


Chain C from PDB  Type:PROTEIN  Length:253
 aligned with KDUI1_ENTFA | Q838L9 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:261
                              1                                                                                                                                                                                                                                                                  
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258 
         KDUI1_ENTFA      - --METRYTHSPADIRHYSTEQLRDEFLVEKVFIPGAISLTYTHNDRMIFGGVTPTTEELEIILDKELGVDYFLERRELGVINIGGPGFIEIDGAKETMKKQDGYYIGKETKHVRFSSENPDNPAKFYISCVPAHHKYPNVKISIDEITPMETGDPLTLNQRKIYQYIHPNVCESCQLQMGYTILEPGSAWNTMPCHTHERRMEAYVYFDMEEDTRIFHMMGKPDETKHLVMSNEQAAISPSWSIHSGVGTSNYSFIWAMCG  259
               SCOP domains d1ywkc_ C: 5-keto-4-deoxyuronate isomerase KduI                                                                                                                                                                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhh..hhhhhhhhhee........eeeeee....eeeeee......ee...hhhhh.......eeeeeee....eeeee..eeeee....eeee......eeeee........eeeeeee.......eee...........hhhhh..eeeeeee..........eeeeeee........--------.eeeeeee.......eeeee......eeeee...eeeee.......eee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ywk C  999 QNMETRYTHSPADIRHYSTEQLRDEFLVEKVFIPGAISLTYTHNDRMIFGGVTPTTEELEIILDKELGVDYFLERRELGVINIGGPGFIEIDGAKETMKKQDGYYIGKETKHVRFSSENPDNPAKFYISCVPAHHKYPNVKISIDEITPMETGDPLTLNQRKIYQYIHPNVCESCQLQMGYTILEPGSAWNT--------RMEAYVYFDMEEDTRIFHMMGKPDETKHLVMSNEQAAISPSWSIHSGVGTSNYSFIWAMCG 1259
                                  1008      1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118      1128      1138      1148      1158      1168      1178      1188 |       -|     1208      1218      1228      1238      1248      1258 
                                                                                                                                                                                                                        1190     1199                                                            


Chain D from PDB  Type:PROTEIN  Length:254
 aligned with KDUI1_ENTFA | Q838L9 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:262
                              1                                                                                                                                                                                                                                                                   
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258  
         KDUI1_ENTFA      - --METRYTHSPADIRHYSTEQLRDEFLVEKVFIPGAISLTYTHNDRMIFGGVTPTTEELEIILDKELGVDYFLERRELGVINIGGPGFIEIDGAKETMKKQDGYYIGKETKHVRFSSENPDNPAKFYISCVPAHHKYPNVKISIDEITPMETGDPLTLNQRKIYQYIHPNVCESCQLQMGYTILEPGSAWNTMPCHTHERRMEAYVYFDMEEDTRIFHMMGKPDETKHLVMSNEQAAISPSWSIHSGVGTSNYSFIWAMCGE  260
               SCOP domains d1ywkd_ D: 5-keto-4-deoxyuronate isomerase KduI                                                                                                                                                                                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhh..hhhhhhhhhee........eeeeee....eeeeee......ee...hhhhh.......eeeeeee....eeeee..eeeee....eeee......eeeee........eeeeeee.......eeehhhhh......hhhhh..eeeeeee..........eeeeeee........--------.eeeeeee.......eeeee......eeeee...eeeee.......eee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ywk D  999 QNMETRYTHSPADIRHYSTEQLRDEFLVEKVFIPGAISLTYTHNDRMIFGGVTPTTEELEIILDKELGVDYFLERRELGVINIGGPGFIEIDGAKETMKKQDGYYIGKETKHVRFSSENPDNPAKFYISCVPAHHKYPNVKISIDEITPMETGDPLTLNQRKIYQYIHPNVCESCQLQMGYTILEPGSAWNT--------RMEAYVYFDMEEDTRIFHMMGKPDETKHLVMSNEQAAISPSWSIHSGVGTSNYSFIWAMCGE 1260
                                  1008      1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118      1128      1138      1148      1158      1168      1178      1188 |       -|     1208      1218      1228      1238      1248      1258  
                                                                                                                                                                                                                        1190     1199                                                             


Chain E from PDB  Type:PROTEIN  Length:254
 aligned with KDUI1_ENTFA | Q838L9 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:263
                               1                                                                                                                                                                                                                                                                   
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257   
         KDUI1_ENTFA      - ---METRYTHSPADIRHYSTEQLRDEFLVEKVFIPGAISLTYTHNDRMIFGGVTPTTEELEIILDKELGVDYFLERRELGVINIGGPGFIEIDGAKETMKKQDGYYIGKETKHVRFSSENPDNPAKFYISCVPAHHKYPNVKISIDEITPMETGDPLTLNQRKIYQYIHPNVCESCQLQMGYTILEPGSAWNTMPCHTHERRMEAYVYFDMEEDTRIFHMMGKPDETKHLVMSNEQAAISPSWSIHSGVGTSNYSFIWAMCGE  260
               SCOP domains d1ywke_ E: 5-keto-4-deoxyuronate isomerase KduI                                                                                                                                                                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...........hhhhhhhhhee........eeeeee....eeeeee......ee...hhhhh.......eeeeeee....eeeee..eeeee....eeee......eeeee........eeeeeee.......eee...........hhhhh..eeeeeee..........eeeeeee........---------.eeeeee.......eeeee......eeeee...eeeee.......eee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ywk E  998 LQNMETRYTHSPADIRHYSTEQLRDEFLVEKVFIPGAISLTYTHNDRMIFGGVTPTTEELEIILDKELGVDYFLERRELGVINIGGPGFIEIDGAKETMKKQDGYYIGKETKHVRFSSENPDNPAKFYISCVPAHHKYPNVKISIDEITPMETGDPLTLNQRKIYQYIHPNVCESCQLQMGYTILEPGSAWNT---------MEAYVYFDMEEDTRIFHMMGKPDETKHLVMSNEQAAISPSWSIHSGVGTSNYSFIWAMCGE 1260
                                  1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      1147      1157      1167      1177      1187  |      -  |   1207      1217      1227      1237      1247      1257   
                                                                                                                                                                                                                         1190      1200                                                            


Chain F from PDB  Type:PROTEIN  Length:253
 aligned with KDUI1_ENTFA | Q838L9 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:262
                              1                                                                                                                                                                                                                                                                   
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258  
         KDUI1_ENTFA      - --METRYTHSPADIRHYSTEQLRDEFLVEKVFIPGAISLTYTHNDRMIFGGVTPTTEELEIILDKELGVDYFLERRELGVINIGGPGFIEIDGAKETMKKQDGYYIGKETKHVRFSSENPDNPAKFYISCVPAHHKYPNVKISIDEITPMETGDPLTLNQRKIYQYIHPNVCESCQLQMGYTILEPGSAWNTMPCHTHERRMEAYVYFDMEEDTRIFHMMGKPDETKHLVMSNEQAAISPSWSIHSGVGTSNYSFIWAMCGE  260
               SCOP domains d1ywkf_ F: 5-keto-4-deoxyuronate isomerase KduI                                                                                                                                                                                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...........hhhhhhhhhee........eeeeee....eeeeee......ee...hhhhh.......eeeeeee....eeeee..eeeee....eeee......eeeee........eeeeeee.......eee...........hhhhh..eeeeeee..........eeeeeee........---------.eeeeee.......eeeee......eeeee...eeeee.......eee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ywk F  999 QNMETRYTHSPADIRHYSTEQLRDEFLVEKVFIPGAISLTYTHNDRMIFGGVTPTTEELEIILDKELGVDYFLERRELGVINIGGPGFIEIDGAKETMKKQDGYYIGKETKHVRFSSENPDNPAKFYISCVPAHHKYPNVKISIDEITPMETGDPLTLNQRKIYQYIHPNVCESCQLQMGYTILEPGSAWNT---------MEAYVYFDMEEDTRIFHMMGKPDETKHLVMSNEQAAISPSWSIHSGVGTSNYSFIWAMCGE 1260
                                  1008      1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118      1128      1138      1148      1158      1168      1178      1188 |       - |    1208      1218      1228      1238      1248      1258  
                                                                                                                                                                                                                        1190      1200
   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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YWK)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (KDUI1_ENTFA | Q838L9)
molecular function
    GO:0008697    4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase activity    Catalysis of the reaction: 5-dehydro-4-deoxy-D-glucuronate = 3-deoxy-D-glycero-2,5-hexodiulosonate.
    GO:0016861    intramolecular oxidoreductase activity, interconverting aldoses and ketoses    Catalysis of an oxidation-reduction (redox) reaction in which the hydrogen donor and acceptor, which is an aldose or a ketose, are the same molecule, and no oxidized product appears.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0045490    pectin catabolic process    The chemical reactions and pathways resulting in the breakdown of pectin, a polymer containing a backbone of alpha-1,4-linked D-galacturonic acid residues.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1ywk)
 
  Sites
(no "Sites" information available for 1ywk)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ywk)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]
    Biological Unit 5  [ Jena3D ]
    Biological Unit 6  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 PNG format | Biol. Unit 5 PNG format | Biol. Unit 6 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1ywk
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  KDUI1_ENTFA | Q838L9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  5.3.1.17
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  KDUI1_ENTFA | Q838L9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1YWK)

(-) Related Entries Specified in the PDB File

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