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

(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE SUGAR BINDING PROTEIN (YP_001300177.1) FROM BACTEROIDES VULGATUS ATCC 8482 AT 1.70 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  23 Oct 09  (Deposition) - 24 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Putative Sugar Binding Protein, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Sugar Binding Protein (Yp_001300177. 1) From Bacteroides Vulgatus Atcc 8482 At 1. 7 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE SUGAR BINDING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BVU_2916
    Organism Scientific: BACTEROIDES VULGATUS ATCC 8482
    Organism Taxid: 435590
    Strain: ATCC 8482 / DSM 1447 / NCTC 11154

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 16)

Asymmetric Unit (5, 16)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
4MSE5Mod. Amino AcidSELENOMETHIONINE
5PO47Ligand/IonPHOSPHATE ION
Biological Unit 1 (4, 30)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3MRD2Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
4MSE10Mod. Amino AcidSELENOMETHIONINE
5PO414Ligand/IonPHOSPHATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:-1 , ARG A:26 , HOH A:433BINDING SITE FOR RESIDUE CL A 300
02AC2SOFTWAREHOH A:411 , HOH A:422 , HOH A:594 , HOH A:611BINDING SITE FOR RESIDUE MPD A 301
03AC3SOFTWARELYS A:104 , ARG A:110 , PHE A:172 , HOH A:411 , HOH A:422 , HOH A:594 , HOH A:611BINDING SITE FOR RESIDUE MRD A 302
04AC4SOFTWARETHR A:147 , ASN A:194 , ARG A:208BINDING SITE FOR RESIDUE MPD A 303
05AC5SOFTWARELEU A:24 , ASN A:195 , HOH A:523BINDING SITE FOR RESIDUE PO4 A 304
06AC6SOFTWAREARG A:40 , HOH A:438 , HOH A:478 , HOH A:531BINDING SITE FOR RESIDUE PO4 A 305
07AC7SOFTWARELEU A:50 , THR A:51 , ASP A:52 , LYS A:85 , GLN A:127 , HOH A:482 , HOH A:524 , HOH A:550BINDING SITE FOR RESIDUE PO4 A 306
08AC8SOFTWAREASP A:129 , ASP A:133 , MSE A:141 , ARG A:170 , HOH A:399 , HOH A:400BINDING SITE FOR RESIDUE PO4 A 307
09AC9SOFTWARELYS A:155 , GLU A:157 , ASN A:178 , SER A:179 , HOH A:389 , HOH A:398 , HOH A:579BINDING SITE FOR RESIDUE PO4 A 308
10BC1SOFTWARETYR A:144 , GLU A:156 , HOH A:401BINDING SITE FOR RESIDUE PO4 A 309
11BC2SOFTWARESER A:120 , TYR A:122 , LEU A:123BINDING SITE FOR RESIDUE PO4 A 310

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KDW)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KDW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KDW)

(-) 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:206
 aligned with A6L4E1_BACV8 | A6L4E1 from UniProtKB/TrEMBL  Length:222

    Alignment length:206
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214      
         A6L4E1_BACV8    15 VVITAGAVDLDREGRDPAYVESIVKRSQKIVDKLELTDTVAAREVTTIIANRYFKLNDIYETRDAKVKLAKETLTGDAKQEAVKAAEAEKDAALYRTHFAFPADLSLYLDAKQIDAVKDGMTYGVVMVTYKATVDMIPTLKEEEKAQIMAWLVEAREFAMDAENSNKKHAAFGKYKGRINNYLSKRGYDLVKERKAWYERIKARGG 220
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------DUF3826-3kdwA01 A:32-217                                                                                                                                                                  --- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kdw A  -5 NLYFQGAVDLDREGRDPAYVESIVKRSQKIVDKLELTDTVAAREVTTIIANRYFKLNDIYETRDAKVKLAKETLTGDAKQEAVKAAEAEKDAALYRTHFAFPADLSLYLDAKQIDAVKDGmTYGVVmVTYKATVDmIPTLKEEEKAQImAWLVEAREFAmDAENSNKKHAAFGKYKGRINNYLSKRGYDLVKERKAWYERIKARGG 220
                                 || 24        34        44        54        64        74        84        94       104       114       124       134|     |144     | 154       164       174       184       194       204       214      
                                 0|                                                                                                               135-MSE |      150-MSE      163-MSE    174-MSE                                          
                                 21                                                                                                                     141-MSE
   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 3KDW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: DUF3826] (1)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3KDW)

 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MPD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MRD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ 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
(no "Cis Peptide Bonds" information available for 3kdw)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  3kdw
    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
  A6L4E1_BACV8 | A6L4E1
    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
  A6L4E1_BACV8 | A6L4E1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3KDW)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3KDW)