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

(-) Description

Title :  CRYSTAL STRUCTURE OF BARLEY BETA-D-GLUCAN GLUCOHYDROLASE ISOENZYME EXO1 IN COMPLEX WITH 4-DEOXY-GLUCOSE
 
Authors :  V. A. Streltsov, M. Hrmova
Date :  12 Nov 13  (Deposition) - 25 Mar 15  (Release) - 25 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  X
Keywords :  Beta Barrel, Hydrolase, Grain Development, Enzyme Function Initiative, Tim Barrel/Beta Sheet, N-Glycosylation, Plant Apoplast (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. A. Streltsov, S. Luang, J. R. Ketudat-Cairns, M. Raab, I. Tvaroska, S. Fort, J. Jimenez-Barbero, A. Peisley, J. N. Varghese, M. Hrmova
A Landscape Of The Product And Substrate Trajectories In A Glycoside Hydrolase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BETA-D-GLUCAN EXOHYDROLASE ISOENZYME EXOI
    Chains: X
    EC Number: 3.2.1.-
    Fragment: UNP RESIDUES 26-630
    Organism Common: BARLEY,TWO-ROWED BARLEY
    Organism Scientific: HORDEUM VULGARE SUBSP. VULGARE
    Organism Taxid: 112509

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 21)

Asymmetric/Biological Unit (8, 21)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2BMA3Ligand/IonBETA-D-MANNOSE
3FUL1Ligand/IonBETA-L-FUCOSE
4GOL6Ligand/IonGLYCEROL
5MAN1Ligand/IonALPHA-D-MANNOSE
6NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE
7SO41Ligand/IonSULFATE ION
8XYP1Ligand/IonBETA-D-XYLOPYRANOSE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP X:95 , PHE X:144 , ARG X:158 , LYS X:206 , HIS X:207 , MET X:250 , TYR X:253 , ASP X:285 , MET X:316 , GLU X:491 , GOL X:715 , HOH X:801 , HOH X:802 , HOH X:803 , HOH X:804 , HOH X:805BINDING SITE FOR RESIDUE BGC X 714
02AC2SOFTWAREGLY X:56 , GLY X:57 , TRP X:286 , TRP X:430 , TRP X:434 , GLU X:491 , BGC X:714 , HOH X:803 , HOH X:805 , HOH X:869BINDING SITE FOR RESIDUE GOL X 715
03AC3SOFTWAREARG X:386 , LYS X:387 , FUL X:711BINDING SITE FOR RESIDUE GOL X 716
04AC4SOFTWARETHR X:24 , ALA X:26 , ARG X:382 , GLN X:551 , HOH X:850 , HOH X:909 , HOH X:1097 , HOH X:1287BINDING SITE FOR RESIDUE GOL X 717
05AC5SOFTWAREARG X:22 , THR X:24 , HOH X:899 , HOH X:979 , HOH X:1200BINDING SITE FOR RESIDUE GOL X 718
06AC6SOFTWAREARG X:119 , ARG X:566 , LEU X:593 , GLY X:594 , HOH X:1250 , HOH X:1651BINDING SITE FOR RESIDUE GOL X 719
07AC7SOFTWAREASN X:48 , GLN X:322 , ILE X:325 , SER X:326 , GLN X:375 , GLU X:376 , ASP X:379 , HOH X:1431 , HOH X:1481 , HOH X:1587BINDING SITE FOR RESIDUE GOL X 720
08AC8SOFTWAREPRO X:338 , MET X:339 , SER X:340 , HOH X:1403BINDING SITE FOR RESIDUE SO4 X 721
09AC9SOFTWAREGLU X:220 , ASN X:221 , THR X:294 , HOH X:883 , HOH X:1026 , HOH X:1137 , HOH X:1299 , HOH X:1321 , HOH X:1619 , HOH X:1655 , HOH X:1656 , HOH X:1667 , HOH X:1677BINDING SITE FOR CHAIN X OF SUGAR BOUND TO ASN X 221 RESIDUES 701 TO 703
10BC1SOFTWARETYR X:425 , HIS X:487 , ASN X:496 , ASN X:498 , PRO X:502 , GLU X:503 , HOH X:1042 , HOH X:1047 , HOH X:1087 , HOH X:1280 , HOH X:1284 , HOH X:1426 , HOH X:1441 , HOH X:1474 , HOH X:1503 , HOH X:1535 , HOH X:1596 , HOH X:1628BINDING SITE FOR CHAIN X OF SUGAR BOUND TO ASN X 498 RESIDUES 704 TO 708
11BC2SOFTWARETHR X:118 , ARG X:119 , ARG X:566 , ASN X:600 , GOL X:716 , HOH X:860 , HOH X:954 , HOH X:1046 , HOH X:1063 , HOH X:1207 , HOH X:1374 , HOH X:1522 , HOH X:1594 , HOH X:1672BINDING SITE FOR CHAIN X OF SUGAR BOUND TO ASN X 600 RESIDUES 709 TO 713

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1X:151 -X:159
2X:513 -X:518

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Ala X:145 -Pro X:146
2Lys X:206 -His X:207
3Phe X:208 -Val X:209
4Thr X:294 -Pro X:295
5Val X:317 -Pro X:318
6Leu X:404 -Pro X:405
7Glu X:503 -Pro X:504
8Leu X:578 -Pro X:579

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WLK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WLK)

(-) Exons   (0, 0)

(no "Exon" information available for 3WLK)

(-) 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 X from PDB  Type:PROTEIN  Length:602
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...hhhhhhhhhhh..hhhhhhhhheeee.hhhhhhhhhhh...eeee..........hhhhhhhhhhhhhhhhhh.......eeee................hhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..............hhhhh...hhhhhhhh.hhhhhhhh.....................eeeee.hhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhh...eeee...ee..ee...hhhhhh...........eee.....hhhhh.....hhhhhhhhhhhhh...ee...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh........hhhhhhhh.hhhhhhhhhhhhhhhheeeee.................eeeee.....hhhhhhh.................hhhhhhhhhh....eeeee...hhhhhhhh....eeeeee....hhhhhh.........hhhhhhhhhh...eeeeee......hhhhhhhh.eeeeee.....hhhhhhhhh...............hhhhh........................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wlk X   1 DYVLYKDATKPVEDRVADLLGRMTLAEKIGQMTQIERLVATPDVLRDNFIGSLLSGGGSVPRKGATAKEWQDMVDGFQKACMSTRLGIPMIYGIDAVHGQNNVYGATIFPHNVGLGATRDPYLVKRIGEATALEVRATGIQYAFAPCIAVCRDPRWGRCYESYSEDRRIVQSMTELIPGLQGDVPKDFTSGMPFVAGKNKVAACAKHFVGDGGTVDGINENNTIINREGLMNIHMPAYKNAMDKGVSTVMISYSSWNGVKMHANQDLVTGYLKDTLKFKGFVISDWEGIDRITTPAGSDYSYSVKASILAGLDMIMVPNKYQQFISILTGHVNGGVIPMSRIDDAVTRILRVKFTMGLFENPYADPAMAEQLGKQEHRDLAREAARKSLVLLKNGKTSTDAPLLPLPKKAPKILVAGSHADNLGYQCGGWTIEWQGDTGRTTVGTTILEAVKAAVDPSTVVVFAENPDAEFVKSGGFSYAIVAVGEHPYTETKGDNLNLTIPEPGLSTVQAVCGGVRCATVLISGRPVVVQPLLAASDALVAAWLPGSEGQGVTDALFGDFGFTGRLPRTWFKSVDQLPMNVGDAHYDPLFRLGYGLTTNAT 602
                                    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
   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 3WLK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WLK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WLK)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    BGC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    BMA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FUL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MAN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    XYP  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala X:145 - Pro X:146   [ RasMol ]  
    Glu X:503 - Pro X:504   [ RasMol ]  
    Leu X:404 - Pro X:405   [ RasMol ]  
    Leu X:578 - Pro X:579   [ RasMol ]  
    Lys X:206 - His X:207   [ RasMol ]  
    Phe X:208 - Val X:209   [ RasMol ]  
    Thr X:294 - Pro X:295   [ RasMol ]  
    Val X:317 - Pro X:318   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  3wlk
    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
  Q9XEI3_HORVV | Q9XEI3
    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)
  3.2.1.-
    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
  Q9XEI3_HORVV | Q9XEI3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9XEI3_HORVV | Q9XEI3: 1ex1 1ieq 1iev 1iew 1iex 1j8v 1lq2 1x38 1x39 3wlh 3wli 3wlj 3wll 3wlm 3wln 3wlo 3wlp 3wlq 3wlr 3wls 3wlt

(-) Related Entries Specified in the PDB File

1ex1 1ieq 1iev 1iew 1iex 1j8v 3wlh 3wli 3wlj 3wll 3wlm 3wln 3wlo 3wlp 3wlq 3wlr 3wls 3wlt