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(-) Description

Title :  CRYSTAL STRUCTURE OF PULLULANASE TYPE I FROM BACILLUS SUBTILIS STR. 168 COMPLEXED WITH ALPHA-CYCLODEXTRIN
 
Authors :  B. Mikami, D. Malle, S. Utsumi, H. Iwamoto, Y. Katsuya
Date :  24 Jan 07  (Deposition) - 19 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Multiple Domain, Beta-Alpha-Barrel, Alpha-Amylase-Family, Alpha- Cyclodextrin, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Malle, H. Iwamoto, Y. Katsuya, S. Utsumi, B. Mikami
Crystal Structure Of Pullulanase Type I From Bacillus Subtilis Str. 168 In Complex With Maltose And Alpha-Cyclodextrin
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AMYX PROTEIN
    Chains: A, B
    EC Number: 3.2.1.41
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21D
    Expression System Strain: HMS 174
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AMYX
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: 168
    Synonym: PULLULANASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 18)

Asymmetric Unit (4, 18)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CA2Ligand/IonCALCIUM ION
3GLC12Ligand/IonALPHA-D-GLUCOSE
4GOL2Ligand/IonGLYCEROL
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3GLC6Ligand/IonALPHA-D-GLUCOSE
4GOL1Ligand/IonGLYCEROL
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3GLC6Ligand/IonALPHA-D-GLUCOSE
4GOL1Ligand/IonGLYCEROL

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:437 , ASN A:526 , GLC A:722 , GLC A:726BINDING SITE FOR RESIDUE GLC A 721
02AC2SOFTWARETRP A:437 , ASP A:465 , ARG A:468 , PHE A:476 , GLC A:721 , GLC A:723BINDING SITE FOR RESIDUE GLC A 722
03AC3SOFTWAREASP A:469 , ASN A:474 , PHE A:476 , GLC A:722 , GLC A:724BINDING SITE FOR RESIDUE GLC A 723
04AC4SOFTWAREASN A:474 , PHE A:476 , HIS A:477 , GLC A:723 , GLC A:725BINDING SITE FOR RESIDUE GLC A 724
05AC5SOFTWAREPHE A:476 , GLC A:724 , GLC A:726BINDING SITE FOR RESIDUE GLC A 725
06AC6SOFTWAREASN A:526 , GLU A:579 , GLC A:721 , GLC A:725BINDING SITE FOR RESIDUE GLC A 726
07AC7SOFTWARETRP B:437 , PHE B:476 , ASN B:526 , GLC B:732 , GLC B:736BINDING SITE FOR RESIDUE GLC B 731
08AC8SOFTWARETRP B:437 , LEU B:439 , ASP B:465 , ARG B:468 , PHE B:476 , GLC B:731 , GLC B:733BINDING SITE FOR RESIDUE GLC B 732
09AC9SOFTWAREASP B:469 , ASN B:474 , PHE B:476 , GLC B:732 , GLC B:734 , HOH B:1429BINDING SITE FOR RESIDUE GLC B 733
10BC1SOFTWAREHIS B:477 , GLC B:733 , GLC B:735 , HOH B:1429BINDING SITE FOR RESIDUE GLC B 734
11BC2SOFTWAREPHE B:476 , GLC B:734 , GLC B:736BINDING SITE FOR RESIDUE GLC B 735
12BC3SOFTWAREGLU B:579 , GLC B:731 , GLC B:735 , HOH B:1427 , HOH B:1428BINDING SITE FOR RESIDUE GLC B 736
13BC4SOFTWAREASP A:275 , PHE A:276 , GLU A:281 , GLU A:301 , HOH A:812 , HOH A:825 , HOH A:1270BINDING SITE FOR RESIDUE CA A 741
14BC5SOFTWARETRP A:530 , ASP A:542 , ARG A:546 , ARG A:595 , PHE A:599BINDING SITE FOR RESIDUE ACT A 751
15BC6SOFTWAREASP B:275 , PHE B:276 , GLU B:281 , GLU B:301 , HOH B:897 , HOH B:954 , HOH B:1396BINDING SITE FOR RESIDUE CA B 742
16BC7SOFTWARETRP B:530 , ASP B:542 , ARG B:546 , PHE B:599BINDING SITE FOR RESIDUE ACT B 752
17BC8SOFTWAREARG A:223 , GLY A:237 , LYS A:238 , PRO A:284 , LEU A:285 , SER A:303 , HOH A:910BINDING SITE FOR RESIDUE GOL A 761
18BC9SOFTWAREPHE B:69 , GLY B:70 , LYS B:71 , HIS B:73 , LEU B:85 , GLN B:86 , ILE B:87 , ALA B:123 , THR B:125 , HOH B:883BINDING SITE FOR RESIDUE GOL B 762

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2E8Z)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:32 -Pro A:33
2Pro B:32 -Pro B:33

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2E8Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2E8Z)

(-) Exons   (0, 0)

(no "Exon" information available for 2E8Z)

(-) 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:712
 aligned with PULA_BACSU | C0SPA0 from UniProtKB/Swiss-Prot  Length:718

    Alignment length:712
                                    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       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710  
           PULA_BACSU     1 MVSIRRSFEAYVDDMNIITVLIPAEQKEIMTPPFRLETEITDFPLAVREEYSLEAKYKYVCVSDHPVTFGKIHCVRASSGHKTDLQIGAVIRTAAFDDEFYYDGELGAVYTADHTVFKVWAPAATSAAVKLSHPNKSGRTFQMTRLEKGVYAVTVTGDLHGYEYLFCICNNSEWMETVDQYAKAVTVNGEKGVVLRPDQMKWTAPLKPFSHPVDAVIYETHLRDFSIHENSGMINKGKYLALTETDTQTANGSSSGLAYVKELGVTHVELLPVNDFAGVDEEKPLDAYNWGYNPLHFFAPEGSYASNPHDPQTRKTELKQMINTLHQHGLRVILDVVFNHVYKRENSPFEKTVPGYFFRHDECGMPSNGTGVGNDIASERRMARKFIADCVVYWLEEYNVDGFRFDLLGILDIDTVLYMKEKATKAKPGILLFGEGWDLATPLPHEQKAALANAPRMPGIGFFNDMFRDAVKGNTFHLKATGFALGNGESAQAVMHGIAGSSGWKALAPIVPEPSQSINYVESHDNHTFWDKMSFALPQENDSRKRSRQRLAAAIILLAQGVPFIHSGQEFFRTKQGVENSYQSSDSINQLDWDRRETFKEDVHYIRRLISLRKAHPAFRLRSAADIQRHLECLTLKEHLIAYRLYDLDEVDEWKDIIVIHHASPDSVEWRLPNDIPYRLLCDPSGFQEDPTEIKKTVAVNGIGTVILYLAS 712
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee..eeeeeee.hhh......eeee....eeeeeeeeeeee..eeeeeee...........eee.....eee.ee.hhhhhhhhhhhhh.....eeee...eeeeeee.....eeeeeee......eeee.ee....eeeeeee......eeeeeeee..eeeee........hhhhh.ee.................hhhhh.eeee..hhhhhh.........hhhhhhh..........hhhhhhhhhh..eeee...eee......hhhhh......eeeeeee.........hhhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhh..........................hhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhh...eeee.........hhhhh.hhhhhhhh...eeehhhhhhhhhh........hhhhhhhhhhhhhhhhhh.............hhh.eee........hhhhhhhhhh...hhhhhhhhhhhhhhhhhh...eeeee.hhhhh............hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhheeeeee...eeeeee........eeeeeeeee....eeeee......eeeeee..eeeeeeeee..eeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e8z A   1 MVSIRRSFEAYVDDMNIITVLIPAEQKEIMTPPFRLETEITDFPLAVREEYSLEAKYKYVCVSDHPVTFGKIHCVRASSGHKTDLQIGAVIRTAAFDDEFYYDGELGAVYTADHTVFKVWAPAATSAAVKLSHPNKSGRTFQMTRLEKGVYAVTVTGDLHGYEYLFCICNNSEWMETVDQYAKAVTVNGEKGVVLRPDQMKWTAPLKPFSHPVDAVIYETHLRDFSIHENSGMINKGKYLALTETDTQTANGSSSGLAYVKELGVTHVELLPVNDFAGVDEEKPLDAYNWGYNPLHFFAPEGSYASNPHDPQTRKTELKQMINTLHQHGLRVILDVVFNHVYKRENSPFEKTVPGYFFRHDECGKPSNGTGVGNDIASERRMARKFIADCVVYWLEEYNVDGFRFDLLGILDIDTVLYMKEKATKAKPGILLFGEGWDLATPLPHEQKAALANAPRMPGIGFFNDMFRDAVKGNTFHLKATGFALGNGESAQAVMHGIAGSSGWKALAPIVPEPSQSINYVESHDNHTFWDKMSFALPQENDSRKRSRQRLAVAIILLAQGVPFIHSGQEFFRTKQGVENSYQSSDSINQLDWDRRETFKEDVHYIRRLISLRKAHPAFRLRSAADIQRHLECLTLKEHLIAYRLYDLDEVDEWKDIIVIHHASPDSVEWRLPNDIPYRLLCDPSGFQEDPTEIKKTVAVNGIGTVILYLAS 712
                                    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       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710  


Chain B from PDB  Type:PROTEIN  Length:712
 aligned with PULA_BACSU | C0SPA0 from UniProtKB/Swiss-Prot  Length:718

    Alignment length:712
                                    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       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710  
           PULA_BACSU     1 MVSIRRSFEAYVDDMNIITVLIPAEQKEIMTPPFRLETEITDFPLAVREEYSLEAKYKYVCVSDHPVTFGKIHCVRASSGHKTDLQIGAVIRTAAFDDEFYYDGELGAVYTADHTVFKVWAPAATSAAVKLSHPNKSGRTFQMTRLEKGVYAVTVTGDLHGYEYLFCICNNSEWMETVDQYAKAVTVNGEKGVVLRPDQMKWTAPLKPFSHPVDAVIYETHLRDFSIHENSGMINKGKYLALTETDTQTANGSSSGLAYVKELGVTHVELLPVNDFAGVDEEKPLDAYNWGYNPLHFFAPEGSYASNPHDPQTRKTELKQMINTLHQHGLRVILDVVFNHVYKRENSPFEKTVPGYFFRHDECGMPSNGTGVGNDIASERRMARKFIADCVVYWLEEYNVDGFRFDLLGILDIDTVLYMKEKATKAKPGILLFGEGWDLATPLPHEQKAALANAPRMPGIGFFNDMFRDAVKGNTFHLKATGFALGNGESAQAVMHGIAGSSGWKALAPIVPEPSQSINYVESHDNHTFWDKMSFALPQENDSRKRSRQRLAAAIILLAQGVPFIHSGQEFFRTKQGVENSYQSSDSINQLDWDRRETFKEDVHYIRRLISLRKAHPAFRLRSAADIQRHLECLTLKEHLIAYRLYDLDEVDEWKDIIVIHHASPDSVEWRLPNDIPYRLLCDPSGFQEDPTEIKKTVAVNGIGTVILYLAS 712
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee..eeeeeee.hhh.......eee....eee.eeeeeee...eeeeeee...........eee.....eeeeee.hhhhhhhhhhhhh.....eeee...eeeeeee.....eeeeeee......eeee.ee....eeeeeee......eeeeeeee..eeeee........hhhhh.ee.................hhhhh.eeeehhhhhhhh.........hhhhhhh..........hhhhhhhhhh..eeee...eee......hhhhh......eeeeeee.........hhhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhh..........................hhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhh...eeee.........hhhhh.hhhhhhhh...eeehhhhhhhhhh........hhhhhhhhhhhhhhhhhh.............hhh.eee........hhhhhhhhhh...hhhhhhhhhhhhhhhhhh...eeeee.hhhhh............hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhheeeeeee..eeeeee..........eeeeeee....eeeee......eeeeee..eeeeeeeee..eeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e8z B   1 MVSIRRSFEAYVDDMNIITVLIPAEQKEIMTPPFRLETEITDFPLAVREEYSLEAKYKYVCVSDHPVTFGKIHCVRASSGHKTDLQIGAVIRTAAFDDEFYYDGELGAVYTADHTVFKVWAPAATSAAVKLSHPNKSGRTFQMTRLEKGVYAVTVTGDLHGYEYLFCICNNSEWMETVDQYAKAVTVNGEKGVVLRPDQMKWTAPLKPFSHPVDAVIYETHLRDFSIHENSGMINKGKYLALTETDTQTANGSSSGLAYVKELGVTHVELLPVNDFAGVDEEKPLDAYNWGYNPLHFFAPEGSYASNPHDPQTRKTELKQMINTLHQHGLRVILDVVFNHVYKRENSPFEKTVPGYFFRHDECGKPSNGTGVGNDIASERRMARKFIADCVVYWLEEYNVDGFRFDLLGILDIDTVLYMKEKATKAKPGILLFGEGWDLATPLPHEQKAALANAPRMPGIGFFNDMFRDAVKGNTFHLKATGFALGNGESAQAVMHGIAGSSGWKALAPIVPEPSQSINYVESHDNHTFWDKMSFALPQENDSRKRSRQRLAVAIILLAQGVPFIHSGQEFFRTKQGVENSYQSSDSINQLDWDRRETFKEDVHYIRRLISLRKAHPAFRLRSAADIQRHLECLTLKEHLIAYRLYDLDEVDEWKDIIVIHHASPDSVEWRLPNDIPYRLLCDPSGFQEDPTEIKKTVAVNGIGTVILYLAS 712
                                    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       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710
   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  (0, 0)

(no "SCOP Domain" information available for 2E8Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2E8Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2E8Z)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PULA_BACSU | C0SPA0)
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:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    GO:0051060    pullulanase activity    Catalysis of the hydrolysis of (1,6)-alpha-D-glucosidic linkages in pullulan (a linear polymer of alpha-(1,6)-linked maltotriose units) and in amylopectin and glycogen, and the a- and b-limit dextrins of amylopectin and glycogen.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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  2e8z
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  3.2.1.41
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 Related Entries

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

UniProtKB/Swiss-Prot
        PULA_BACSU | C0SPA0: 2e8y 2e9b

(-) Related Entries Specified in the PDB File

2e8y APO ENZYME
2e9b COMPLEXED WITH MALTOSE