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(-) Description

Title :  CRYSTAL STRUCTURE OF L-RHAMNOSE ISOMERASE FROM PSEUDOMONAS STUTZERI WITH METAL ION
 
Authors :  H. Yoshida, M. Yamada, G. Takada, K. Izumori, S. Kamitori
Date :  19 Jun 06  (Deposition) - 19 Dec 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Beta/Alpha Barrel, Tim Barrel, Homo-Tetramer, Metal-Binding Protein, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Yoshida, M. Yamada, Y. Ohyama, G. Takada, K. Izumori, S. Kamitori
The Structures Of L-Rhamnose Isomerase From Pseudomonas Stutzeri In Complexes With L-Rhamnose And D-Allose Provide Insights Into Broad Substrate Specificity
J. Mol. Biol. V. 365 1505 2007
PubMed-ID: 17141803  |  Reference-DOI: 10.1016/J.JMB.2006.11.004
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - L-RHAMNOSE ISOMERASE
    ChainsA, B, C, D
    EC Number5.3.1.14
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    MutationYES
    Organism ScientificPSEUDOMONAS STUTZERI
    Organism Taxid316

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1ZN8Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:219 , ASP A:254 , HIS A:281 , ASP A:327 , HOH A:726 , HOH A:770BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWARELYS A:221 , HIS A:257 , ASP A:289 , HOH A:543 , HOH A:666 , HOH A:726 , HOH A:728BINDING SITE FOR RESIDUE ZN A 502
3AC3SOFTWAREGLU B:219 , ASP B:254 , HIS B:281 , ASP B:327 , HOH B:775 , HOH B:978BINDING SITE FOR RESIDUE ZN B 503
4AC4SOFTWAREHIS B:257 , ASP B:289 , HOH B:632 , HOH B:725 , HOH B:739 , HOH B:775BINDING SITE FOR RESIDUE ZN B 504
5AC5SOFTWAREGLU C:219 , ASP C:254 , HIS C:281 , ASP C:327 , HOH C:644 , HOH C:866BINDING SITE FOR RESIDUE ZN C 505
6AC6SOFTWAREHIS C:257 , ASP C:289 , HOH C:548 , HOH C:571 , HOH C:734 , HOH C:866BINDING SITE FOR RESIDUE ZN C 506
7AC7SOFTWAREGLU D:219 , ASP D:254 , HIS D:281 , ASP D:327 , HOH D:509 , HOH D:593BINDING SITE FOR RESIDUE ZN D 507
8AC8SOFTWAREHIS D:257 , ASP D:289 , HOH D:509 , HOH D:537 , HOH D:579 , HOH D:800BINDING SITE FOR RESIDUE ZN D 508

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2HCV)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Ile A:102 -Pro A:103
2Glu A:224 -Pro A:225
3Ile B:102 -Pro B:103
4Glu B:224 -Pro B:225
5Ile C:102 -Pro C:103
6Glu C:224 -Pro C:225
7Ile D:102 -Pro D:103
8Glu D:224 -Pro D:225

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2HCV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2HCV)

(-) Exons   (0, 0)

(no "Exon" information available for 2HCV)

(-) 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:421
 aligned with Q75WH8_PSEST | Q75WH8 from UniProtKB/TrEMBL  Length:430

    Alignment length:421
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423 
         Q75WH8_PSEST     4 FRIAQDVVARENDRRASALKEDYEALGANLARRGVDIEAVTAKVEKFFVAVPSWGVGTGGTRFARFPGTGEPRGIFDKLDDCAVIQQLTRATPNVSLHIPWDKADPKELKARGDALGLGFDAMNSNTFSDAPGQAHSYKYGSLSHTDAATRAQAVEHNLECIEIGKAIGSKALTVWIGDGSNFPGQSNFTRAFERYLSAMAEIYKGLPDDWKLFSEHKMYEPAFYSTVVQDWGTNYLIAQTLGPKAQCLVDLGHHAPNTNIEMIVARLIQFGKLGGFHFNDSKYGDDDLDAGAIEPYRLFLVFNELVDAEARGVKGFHPAHMIDQSHNVTDPIESLINSANEIRRAYAQALLVDRAALSGYQEDNDALMATETLKRAYRTDVEPILAEARRRTGGAVDPVATYRASGYRARVAAERPASVA 424
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....ee.hhh.................hhhhhhhhhhhhhhhhh...eee........hhhhhhhhhhhhh.ee..ee......................hhhhhhhhhhhhhhhhhhhhhhh..eeee....ee......hhhhhhhhhhhhhhhhhhh.....eeeee.........ee...hhhhhhhhhhhhh..eeeeee.hhh....hhhhhhhhhhhh..eeeeee...............hhhhhhhhhhhhhhhhhh.......eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hcv A   4 FRIAQDVVARENDRRASALKEDYEALGANLARRGVDIEAVTAKVEKFFVAVPSWGVGTGGTRFARFPGTGEPRGIFDKLDDCAVIQQLTRATPNVSLHIPWDKADPKELKARGDALGLGFDAMNSNTFSDAPGQAHSYKYGSLSHTNAATRAQAVEHNLECIEIGKAIGSKALTVWIGDGSNFPGQSNFTRAFERYLSAMAEIYKGLPDDWKLFSEHKMYEPAFYSTVVQDWGTNYLIAQTLGPKAQCLVDLGHHAPNTNIEMIVARLIQFGKLGGFHFNDSKYGDDDLDAGAIEPYRLFLVFNELVDAEARGVKGFHPAHMIDQSHNVTDPIESLINSANEIRRAYAQALLVDRAALSGYQEDNDALMATETLKRAYRTDVEPILAEARRRTGGAVDPVATYRASGYRARVAAERPASVA 424
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423 

Chain B from PDB  Type:PROTEIN  Length:420
 aligned with Q75WH8_PSEST | Q75WH8 from UniProtKB/TrEMBL  Length:430

    Alignment length:420
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423
         Q75WH8_PSEST     4 FRIAQDVVARENDRRASALKEDYEALGANLARRGVDIEAVTAKVEKFFVAVPSWGVGTGGTRFARFPGTGEPRGIFDKLDDCAVIQQLTRATPNVSLHIPWDKADPKELKARGDALGLGFDAMNSNTFSDAPGQAHSYKYGSLSHTDAATRAQAVEHNLECIEIGKAIGSKALTVWIGDGSNFPGQSNFTRAFERYLSAMAEIYKGLPDDWKLFSEHKMYEPAFYSTVVQDWGTNYLIAQTLGPKAQCLVDLGHHAPNTNIEMIVARLIQFGKLGGFHFNDSKYGDDDLDAGAIEPYRLFLVFNELVDAEARGVKGFHPAHMIDQSHNVTDPIESLINSANEIRRAYAQALLVDRAALSGYQEDNDALMATETLKRAYRTDVEPILAEARRRTGGAVDPVATYRASGYRARVAAERPASV 423
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....ee.hhh.................hhhhhhhhhhhhhhhhh...eee........hhhhhhhhhhhhh.ee..ee......................hhhhhhhhhhhhhhhhhhhhhhh..eeee....ee......hhhhhhhhhhhhhhhhhhh.....eeeee.........ee...hhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhh..eeeeee...............hhhhhhhhhhhhhhhhhh.......eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2hcv B   4 FRIAQDVVARENDRRASALKEDYEALGANLARRGVDIEAVTAKVEKFFVAVPSWGVGTGGTRFARFPGTGEPRGIFDKLDDCAVIQQLTRATPNVSLHIPWDKADPKELKARGDALGLGFDAMNSNTFSDAPGQAHSYKYGSLSHTNAATRAQAVEHNLECIEIGKAIGSKALTVWIGDGSNFPGQSNFTRAFERYLSAMAEIYKGLPDDWKLFSEHKMYEPAFYSTVVQDWGTNYLIAQTLGPKAQCLVDLGHHAPNTNIEMIVARLIQFGKLGGFHFNDSKYGDDDLDAGAIEPYRLFLVFNELVDAEARGVKGFHPAHMIDQSHNVTDPIESLINSANEIRRAYAQALLVDRAALSGYQEDNDALMATETLKRAYRTDVEPILAEARRRTGGAVDPVATYRASGYRARVAAERPASV 423
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423

Chain C from PDB  Type:PROTEIN  Length:421
 aligned with Q75WH8_PSEST | Q75WH8 from UniProtKB/TrEMBL  Length:430

    Alignment length:421
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423 
         Q75WH8_PSEST     4 FRIAQDVVARENDRRASALKEDYEALGANLARRGVDIEAVTAKVEKFFVAVPSWGVGTGGTRFARFPGTGEPRGIFDKLDDCAVIQQLTRATPNVSLHIPWDKADPKELKARGDALGLGFDAMNSNTFSDAPGQAHSYKYGSLSHTDAATRAQAVEHNLECIEIGKAIGSKALTVWIGDGSNFPGQSNFTRAFERYLSAMAEIYKGLPDDWKLFSEHKMYEPAFYSTVVQDWGTNYLIAQTLGPKAQCLVDLGHHAPNTNIEMIVARLIQFGKLGGFHFNDSKYGDDDLDAGAIEPYRLFLVFNELVDAEARGVKGFHPAHMIDQSHNVTDPIESLINSANEIRRAYAQALLVDRAALSGYQEDNDALMATETLKRAYRTDVEPILAEARRRTGGAVDPVATYRASGYRARVAAERPASVA 424
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....ee.hhh.................hhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhh.eeeeee......................hhhhhhhhhhhhhhhhhhhhhhh..eeee....ee......hhhhhhhhhhhhhhhhhhh.....eeeee.........ee...hhhhhhhhhhhhh..eeeeee.hhh....hhhhhhhhhhhh..eeeeee...............hhhhhhhhhhhhhhhhhh.......eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hcv C   4 FRIAQDVVARENDRRASALKEDYEALGANLARRGVDIEAVTAKVEKFFVAVPSWGVGTGGTRFARFPGTGEPRGIFDKLDDCAVIQQLTRATPNVSLHIPWDKADPKELKARGDALGLGFDAMNSNTFSDAPGQAHSYKYGSLSHTNAATRAQAVEHNLECIEIGKAIGSKALTVWIGDGSNFPGQSNFTRAFERYLSAMAEIYKGLPDDWKLFSEHKMYEPAFYSTVVQDWGTNYLIAQTLGPKAQCLVDLGHHAPNTNIEMIVARLIQFGKLGGFHFNDSKYGDDDLDAGAIEPYRLFLVFNELVDAEARGVKGFHPAHMIDQSHNVTDPIESLINSANEIRRAYAQALLVDRAALSGYQEDNDALMATETLKRAYRTDVEPILAEARRRTGGAVDPVATYRASGYRARVAAERPASVA 424
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423 

Chain D from PDB  Type:PROTEIN  Length:417
 aligned with Q75WH8_PSEST | Q75WH8 from UniProtKB/TrEMBL  Length:430

    Alignment length:417
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       
         Q75WH8_PSEST     4 FRIAQDVVARENDRRASALKEDYEALGANLARRGVDIEAVTAKVEKFFVAVPSWGVGTGGTRFARFPGTGEPRGIFDKLDDCAVIQQLTRATPNVSLHIPWDKADPKELKARGDALGLGFDAMNSNTFSDAPGQAHSYKYGSLSHTDAATRAQAVEHNLECIEIGKAIGSKALTVWIGDGSNFPGQSNFTRAFERYLSAMAEIYKGLPDDWKLFSEHKMYEPAFYSTVVQDWGTNYLIAQTLGPKAQCLVDLGHHAPNTNIEMIVARLIQFGKLGGFHFNDSKYGDDDLDAGAIEPYRLFLVFNELVDAEARGVKGFHPAHMIDQSHNVTDPIESLINSANEIRRAYAQALLVDRAALSGYQEDNDALMATETLKRAYRTDVEPILAEARRRTGGAVDPVATYRASGYRARVAAERP 420
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....ee.hhh.................hhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhh.eeeeee......................hhhhhhhhhhhhhhhhhhhhhh...eeee....ee......hhhhhhhhhhhhhhhhhhh.....eeeee.........ee...hhhhhhhhhhhhh..eeeeee.hhh....hhhhhhhhhhhh..eeeeee...............hhhhhhhhhhhhhhhhhh.......eeee.......hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hcv D   4 FRIAQDVVARENDRRASALKEDYEALGANLARRGVDIEAVTAKVEKFFVAVPSWGVGTGGTRFARFPGTGEPRGIFDKLDDCAVIQQLTRATPNVSLHIPWDKADPKELKARGDALGLGFDAMNSNTFSDAPGQAHSYKYGSLSHTNAATRAQAVEHNLECIEIGKAIGSKALTVWIGDGSNFPGQSNFTRAFERYLSAMAEIYKGLPDDWKLFSEHKMYEPAFYSTVVQDWGTNYLIAQTLGPKAQCLVDLGHHAPNTNIEMIVARLIQFGKLGGFHFNDSKYGDDDLDAGAIEPYRLFLVFNELVDAEARGVKGFHPAHMIDQSHNVTDPIESLINSANEIRRAYAQALLVDRAALSGYQEDNDALMATETLKRAYRTDVEPILAEARRRTGGAVDPVATYRASGYRARVAAERP 420
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       

   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "SCOP Domain" information available for 2HCV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2HCV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HCV)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q75WH8_PSEST | Q75WH8)
molecular function
    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.

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  2hcv
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 Related Entries

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

UniProtKB/TrEMBL
        Q75WH8_PSEST | Q75WH82i56 2i57 3itl 3ito 3itt 3itv 3itx 3ity 3iud 3iuh 3iui 3m0h 3m0l 3m0m 3m0v 3m0x 3m0y 4gji 4gjj

(-) Related Entries Specified in the PDB File

2i56 THE SAME PROTEIN COMPLEXED WITH L-RHAMNOSE
2i57 THE SAME PROTEIN IN COMPLEX WITH D-ALLOSE