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

(-) Description

Title :  X-RAY STRUCTURE OF GH31 CBM32-2 BOUND TO GALNAC
 
Authors :  J. M. Grondin, K. Abe, A. B. Boraston, S. P. Smith
Date :  11 Aug 14  (Deposition) - 07 Oct 15  (Release) - 08 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Carbohydrate-Binding Module, B-Sandwich, Galnac, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Grondin, D. Duan, A. C. Kirlin, K. T. Abe, S. Chitayat, H. L. Spencer, C. Spencer, A. Campigotto, S. Houliston, C. H. Arrowsmith, J. S. Allingham, A. B. Boraston, S. P. Smith
Diverse Modes Of Galacto-Specific Carbohydrate Recognition By A Family 31 Glycoside Hydrolase From Clostridium Perfringens.
Plos One V. 12 71606 2017
PubMed-ID: 28158290  |  Reference-DOI: 10.1371/JOURNAL.PONE.0171606

(-) Compounds

Molecule 1 - GLYCOSYL HYDROLASE, FAMILY 31/FIBRONECTIN TYPE III DOMAIN PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1323-1470
    Gene: CPF_1301
    Organism Scientific: CLOSTRIDIUM PERFRINGENS
    Organism Taxid: 195103
    Strain: ATCC 13124 / NCTC 8237 / TYPE A

 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  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2GOL2Ligand/IonGLYCEROL
3NGA2Ligand/IonN-ACETYL-D-GALACTOSAMINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL1Ligand/IonGLYCEROL
3NGA1Ligand/IonN-ACETYL-D-GALACTOSAMINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL1Ligand/IonGLYCEROL
3NGA1Ligand/IonN-ACETYL-D-GALACTOSAMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:37 , TRP A:42 , ILE A:43 , ARG A:76 , ALA A:86 , HOH A:301 , HOH A:305 , HOH A:320 , HOH A:325 , HOH A:329 , HOH A:345 , HOH A:371 , HOH A:377 , HOH A:402 , TRP B:42 , NGA B:201binding site for residue NGA A 201
2AC2SOFTWARELYS A:24 , ASP A:27 , THR A:29 , SER A:36 , ASN A:144 , GLU A:145binding site for residue CA A 202
3AC3SOFTWAREASN A:78 , SER A:79 , ASN A:80 , PHE B:44binding site for residue GOL A 203
4AC4SOFTWARETRP A:42 , NGA A:201 , HOH A:335 , ARG B:37 , TRP B:42 , ILE B:43 , ARG B:76 , ALA B:86 , HOH B:302 , HOH B:303 , HOH B:309 , HOH B:313 , HOH B:321 , HOH B:359 , HOH B:368binding site for residue NGA B 201
5AC5SOFTWARELYS B:24 , ASP B:27 , THR B:29 , SER B:36 , ASN B:144 , GLU B:145binding site for residue CA B 202
6AC6SOFTWAREHOH A:343 , ASN B:78 , SER B:79 , ASN B:80binding site for residue GOL B 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4UAP)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:54 -Pro A:55
2Leu B:54 -Pro B:55

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4UAP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UAP)

(-) Exons   (0, 0)

(no "Exon" information available for 4UAP)

(-) 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:150
                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee.hhhhh....hhhhhh......hhhhhee................eeeeeeeeeeeeeeeeeeee............eeeeeeeeee..eeeeeeee......eeeeeeeeeeeeeeeeeeeee.......eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4uap A   3 SHMNITVSGDSSQLQSGMGLDKLIDGTTSSDDSSRMDLKWIFTSDQQDKGTLPFEMTFEFNEPKTLENFTIYNRMNSNGTINIAAMKKVKAVGYLNGEEFDLGEKANITSATTVYELGGKEFDKIVITALDSHKDKNTLAINEIEFYEKS 152
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152


Chain B from PDB  Type:PROTEIN  Length:149
                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.hhhhh....hhhhhh......hhhhhee................eeeeeeeeeeeeeeeeeeee............eeeeeeeeee..eeeeeeee......eeeeeeeeeeeeeeeeeeeee.......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uap B   3 SHMNITVSGDSSQLQSGMGLDKLIDGTTSSDDSSRMDLKWIFTSDQQDKGTLPFEMTFEFNEPKTLENFTIYNRMNSNGTINIAAMKKVKAVGYLNGEEFDLGEKANITSATTVYELGGKEFDKIVITALDSHKDKNTLAINEIEFYEK 151
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142
   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 4UAP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4UAP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4UAP)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4UAP)

 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NGA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:54 - Pro A:55   [ RasMol ]  
    Leu B:54 - Pro B:55   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  4uap
    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
  A0A0H2YST8_C | A0A0H2YST8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  A0A0H2YST8_C | A0A0H2YST8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A0A0H2YST8_C | A0A0H2YST8: 4lks 4lpl 4lqr 4p5y

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4UAP)