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(-) Description

Title :  THE S45A, T46A MUTANT OF THE TYPE I COHESIN-DOCKERIN COMPLEX FROM THE CELLULOSOME OF CLOSTRIDIUM THERMOCELLUM
 
Authors :  A. L. Carvalho, F. M. V. Dias, J. A. M. Prates, L. M. A. Ferreira, H. J. Gilb G. J. Davies, M. J. Romao, C. M. G. A. Fontes
Date :  16 Jan 06  (Deposition) - 13 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.03
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Cell Adhesion, Cohesin/Dockerin Complex, Cellulosome, Cohesin, Dockerin, Clostridium Thermocellum, Scaffolding, Cellulose Degradation, Hydrolase, Glycosidase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. L. Carvalho, F. M. V. Dias, T. Nagy, J. A. M. Prates, M. R. Proctor, N. Smith, E. A. Bayer, G. J. Davies, L. M. A. Ferreira, M. J. Romao, C. M. G. A. Fontes, H. J. Gilbert
Evidence For A Dual Binding Mode Of Dockerin Modules To Cohesins.
Proc. Natl. Acad. Sci. Usa V. 104 3089 2007
PubMed-ID: 17360613  |  Reference-DOI: 10.1073/PNAS.0611173104

(-) Compounds

Molecule 1 - CELLULOSOMAL SCAFFOLDING PROTEIN A
    ChainsA, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentCOHESIN 2 DOMAIN, RESIDUES 181-328
    Organism ScientificCLOSTRIDIUM THERMOCELLUM
    Organism Taxid1515
    SynonymCELLULOSOMAL GLYCOPROTEIN S1/SL, CELLULOSE INTEGRATING PROTEIN A, COHESIN
 
Molecule 2 - ENDO-1,4-BETA-XYLANASE Y
    ChainsB, D
    EC Number3.2.1.8
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRESIDUES 730-791
    MutationYES
    Organism ScientificCLOSTRIDIUM THERMOCELLUM
    Organism Taxid1515
    SynonymXYLANASE Y, XYLY, 1,4-BETA-D-XYLAN XYLANOHYDROLASE Y

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2PO4-1Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:29 , ASP A:98 , HOH A:2163 , HOH A:2164 , HOH A:2165 , HOH A:2166BINDING SITE FOR RESIDUE PO4 A1154
2AC2SOFTWAREPRO A:31 , SER A:32 , LYS A:33 , ASP A:126 , GLN A:132 , HOH A:2167BINDING SITE FOR RESIDUE PO4 A1155
3AC3SOFTWAREASP B:2 , ASN B:4 , ASP B:6 , THR B:8 , ASP B:13 , HOH B:2022BINDING SITE FOR RESIDUE CA B1060
4AC4SOFTWAREASP B:36 , ASP B:38 , ASN B:40 , SER B:42 , ASP B:47 , HOH B:2071BINDING SITE FOR RESIDUE CA B1061
5AC5SOFTWAREASP D:36 , ASP D:38 , ASN D:40 , SER D:42 , ASP D:47 , HOH D:2065BINDING SITE FOR RESIDUE CA D1060
6AC6SOFTWAREASP D:2 , ASN D:4 , ASP D:6 , THR D:8 , ASP D:13 , HOH D:2023BINDING SITE FOR RESIDUE CA D1061

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2CCL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 8)

Asymmetric Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CLOS_CELLULOSOME_RPTPS00448 Clostridium cellulosome enzymes repeated domain signature.XYNY_CLOTM734-753
 
768-787
 
  4B:2-21
D:2-21
B:36-55
D:36-55
2EF_HAND_1PS00018 EF-hand calcium-binding domain.XYNY_CLOTM734-746
 
768-780
 
  4B:2-14
D:2-14
B:36-48
D:36-48
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CLOS_CELLULOSOME_RPTPS00448 Clostridium cellulosome enzymes repeated domain signature.XYNY_CLOTM734-753
 
768-787
 
  2B:2-21
-
B:36-55
-
2EF_HAND_1PS00018 EF-hand calcium-binding domain.XYNY_CLOTM734-746
 
768-780
 
  2B:2-14
-
B:36-48
-
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CLOS_CELLULOSOME_RPTPS00448 Clostridium cellulosome enzymes repeated domain signature.XYNY_CLOTM734-753
 
768-787
 
  2-
D:2-21
-
D:36-55
2EF_HAND_1PS00018 EF-hand calcium-binding domain.XYNY_CLOTM734-746
 
768-780
 
  2-
D:2-14
-
D:36-48

(-) Exons   (0, 0)

(no "Exon" information available for 2CCL)

(-) 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:149
 aligned with CIPA_CLOTH | Q06851 from UniProtKB/Swiss-Prot  Length:1853

    Alignment length:149
                                   192       202       212       222       232       242       252       262       272       282       292       302       312       322         
           CIPA_CLOTH   183 GVVVEIGKVTGSVGTTVEIPVYFRGVPSKGIANCDFVFRYDPNVLEIIGIDPGDIIVDPNPTKSFDTAIYPDRKIIVFLFAEDSGTGAYAITKDGVFAKIRATVKSSAPGYITFDEVGGFADNDLVEQKVSFIDGGVNVGNATPTKGAT 331
               SCOP domains d2ccla_ A: automated matches                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.ee......eeeeeeeee........eeeeeee.....eeeeeeee.......hhhh.eeeeee....eeeeeee.............eeeeeeeeee.....eeeeeeeeeeee........eeee.eee............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ccl A   5 GVVVEIGKVTGSVGTTVEIPVYFRGVPSKGIANCDFVFRYDPNVLEIIGIDPGDIIVDPNPTKSFDTAIYPDRKIIVFLFAEDSGTGAYAITKDGVFAKIRATVKSSAPGYITFDEVGGFADNDLVEQKVSFIDGGVNVGNATPTKLEH 153
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144         

Chain B from PDB  Type:PROTEIN  Length:62
 aligned with XYNY_CLOTM | P51584 from UniProtKB/Swiss-Prot  Length:1077

    Alignment length:62
                                   739       749       759       769       779       789  
           XYNY_CLOTM   730 VLLGDVNGDGTINSTDLTMLKRSVLRAITLTDDAKARADVDKNGSINSTDVLLLSRYLLRVI 791
               SCOP domains ---d2cclb1 B:1-59 Endo-1,4-beta-xylanase Y                     SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhh.....hhhhhhhhh.......hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----EF_HAND_1    ---------------------EF_HAND_1    ----------- PROSITE (1)
                PROSITE (2) ----CLOS_CELLULOSOME_RPT--------------CLOS_CELLULOSOME_RPT---- PROSITE (2)
                 Transcript -------------------------------------------------------------- Transcript
                 2ccl B  -2 VLLGDVNGDGTINSTDLTMLKRSVLRAITLTDDAKARADVDKNGSINAADVLLLSRYLLRVI  59
                                     7        17        27        37        47        57  

Chain C from PDB  Type:PROTEIN  Length:149
 aligned with CIPA_CLOTH | Q06851 from UniProtKB/Swiss-Prot  Length:1853

    Alignment length:149
                                   192       202       212       222       232       242       252       262       272       282       292       302       312       322         
           CIPA_CLOTH   183 GVVVEIGKVTGSVGTTVEIPVYFRGVPSKGIANCDFVFRYDPNVLEIIGIDPGDIIVDPNPTKSFDTAIYPDRKIIVFLFAEDSGTGAYAITKDGVFAKIRATVKSSAPGYITFDEVGGFADNDLVEQKVSFIDGGVNVGNATPTKGAT 331
               SCOP domains d2cclc_ C: automated matches                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.ee......eeeeeeeee......eeeeeeeee.....eeeeeeee.......hhhh.eeeeee....eeeeeee.............eeeeeeeeee.....eeeeeeeeeeeee.......eeee.eee............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ccl C   5 GVVVEIGKVTGSVGTTVEIPVYFRGVPSKGIANCDFVFRYDPNVLEIIGIDPGDIIVDPNPTKSFDTAIYPDRKIIVFLFAEDSGTGAYAITKDGVFAKIRATVKSSAPGYITFDEVGGFADNDLVEQKVSFIDGGVNVGNATPTKLEH 153
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144         

Chain D from PDB  Type:PROTEIN  Length:62
 aligned with XYNY_CLOTM | P51584 from UniProtKB/Swiss-Prot  Length:1077

    Alignment length:62
                                   739       749       759       769       779       789  
           XYNY_CLOTM   730 VLLGDVNGDGTINSTDLTMLKRSVLRAITLTDDAKARADVDKNGSINSTDVLLLSRYLLRVI 791
               SCOP domains d2ccld_ D: automated matches                                   SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhh.....hhhhhhhhh.......hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----EF_HAND_1    ---------------------EF_HAND_1    ----------- PROSITE (1)
                PROSITE (2) ----CLOS_CELLULOSOME_RPT--------------CLOS_CELLULOSOME_RPT---- PROSITE (2)
                 Transcript -------------------------------------------------------------- Transcript
                 2ccl D  -2 VLLGDVNGDGTINSTDLTMLKRSVLRAITLTDDAKARADVDKNGSINAADVLLLSRYLLRVI  59
                                     7        17        27        37        47        57  

   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  (3, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (CIPA_CLOTH | Q06851)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0030248    cellulose binding    Interacting selectively and non-covalently with cellulose.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
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:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0030245    cellulose catabolic process    The chemical reactions and pathways resulting in the breakdown of cellulose, a linear beta1-4 glucan of molecular mass 50-400 kDa with the pyranose units in the -4C1 conformation.
    GO:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Chain B,D   (XYNY_CLOTM | P51584)
molecular function
    GO:0031176    endo-1,4-beta-xylanase activity    Catalysis of the endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans.
    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.
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.
    GO:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
    GO:0045493    xylan catabolic process    The chemical reactions and pathways resulting in the breakdown of xylan, a polymer containing a beta-1,4-linked D-xylose backbone.
cellular component
    GO:0043263    cellulosome    An extracellular multi-enzyme complex containing up to 11 different enzymes aligned on a non-catalytic scaffolding glycoprotein. Functions to hydrolyze cellulose.

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  XYNY_CLOTM | P51584
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 Related Entries

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

UniProtKB/Swiss-Prot
        CIPA_CLOTH | Q068511anu 1aoh 1nbc 1ohz 2b59 3kcp 4b9f 5g5d
        XYNY_CLOTM | P515841dyo 1gkk 1gkl 1h6x 1h6y 1ohz 1wb4 1wb5 1wb6 2w5f 2wys 2wze 3zi7 4bag 4h35 5fxm

(-) Related Entries Specified in the PDB File

1anu COHESIN-2 DOMAIN OF THE CELLULOSOME FROM CLOSTRIDIUM THERMOCELLUM
1aoh SINGLE COHESIN DOMAIN FROM THE SCAFFOLDING PROTEIN CIPA OFTHE CLOSTRIDIUM THERMOCELLUM CELLULOSOME
1dyo XYLAN-BINDING DOMAIN FROM CBM 22, FORMALLY X6B DOMAIN
1gkk FERULOYL ESTERASE DOMAIN OF XYNY FROM CLOSTRIDIUM THERMOCELLUM
1gkl S954A MUTANT OF THE FERULOYL ESTERASE MODULE FROM CLOSTRIDIUM THERMOCELLUM COMPLEXED WITH FERULIC ACID
1h6x THE ROLE OF CONSERVED AMONI ACIDS IN THE CLEFT OF THE C-TERMINAL FAMILY 22 CARBOHYDRATE BINDING MODULE OF CLOSTRIDIUM THERMOCELLUM XYN10B IN LIGAND BINDING
1h6y THE ROLE OF CONSERVED AMONI ACIDS IN THE CLEFT OF THE C-TERMINAL FAMILY 22 CARBOHYDRATE BINDING MODULE OF CLOSTRIDIUM THERMOCELLUM XYN10B IN LIGAND BINDING
1nbc BACTERIAL TYPE 3A CELLULOSE-BINDING DOMAIN
1ohz COHESIN-DOCKERIN COMPLEX FROM THE CELLULOSOME OF CLOSTRIDIUM THERMOCELLUM
1wb4 S954A MUTANT OF THE FERULOYL ESTERASE MODULE FROM CLOSTRIDIUM THERMOCELLUM COMPLEXED WITH SINAPINATE
1wb5 S954A MUTANT OF THE FERULOYL ESTERASE MODULE FROM CLOSTRIDIUM THERMOCELLUM COMPLEXED WITH SYRINGATE
1wb6 S954A MUTANT OF THE FERULOYL ESTERASE MODULE FROM CLOSTRIDIUM THERMOCELLUM COMPLEXED WITH VANILLATE