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 THE COMPLEX OF SIGNALING GLYCOPROTEIN FROM BUFFALO (SPB-40) WITH TETRAHYDROPYRAN AT 2.5 A RESOLUTION
 
Authors :  S. Yamini, A. Chaudhary, M. Sinha, P. Kaur, S. Sharma, T. P. Singh
Date :  06 Sep 13  (Deposition) - 25 Sep 13  (Release) - 25 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Signaling Protein Text Spb-40, Tim Barrel, Signaling Protein, Tetrahydropyran (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Yamini, A. Chaudhary, M. Sinha, P. Kaur, S. Sharma, T. P. Singh
Crystal Structure Of The Complex Of Signaling Glycoprotein From Buffalo (Spb-40) With Tetrahydropyran At 2. 5 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CHITINASE-3-LIKE PROTEIN 1
    Chains: A
    Organism Common: DOMESTIC WATER BUFFALO, RIVER BUFFALO
    Organism Scientific: BUBALUS BUBALIS
    Organism Taxid: 89462
    Synonym: MAMMARY GLAND PROTEIN 40, SPB-40

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
2PYE1Ligand/IonTETRAHYDROPYRAN

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:78 , TYR A:185 , TRP A:331BINDING SITE FOR RESIDUE PYE A 402
2AC2SOFTWAREASN A:39 , ILE A:40 , SER A:41 , TRP A:48 , HOH A:562 , HOH A:575BINDING SITE FOR MONO-SACCHARIDE NAG A 401 BOUND TO ASN A 39

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:5 -A:30
2A:279 -A:343

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ser A:36 -Phe A:37
2Leu A:119 -Trp A:120
3Trp A:331 -Ala A:332

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ML4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ML4)

(-) Exons   (0, 0)

(no "Exon" information available for 4ML4)

(-) 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 A from PDB  Type:PROTEIN  Length:361
                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhh.hhhhh......eeeeeeeeee..eee....hhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhhh......eeeeeee.hhhhhhhhhhhhhhhhhh.eeeee..............................hhhhhhhhhhhh..hhh.eeeeee..eeeeee..........eeee...........eehhhhhhhhhh..eeeee....eeeeee..eeee..hhhhhhhhhhhhhhh...eeeeehhhhh............hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ml4 A   1 YKLICYYTSWSQYREGDGSCFPDAIDPFLCTHVIYSFANISNNEIDTWEWNDVTLYDTLNTLKNRNPNLKTLLSVGGWNYGSQRFSKIASKTQSRRTFIKSVPPFLRTHGFDGLDLAWLWPGWRDKRHLTTLVKEMKAEFVREAQAGTEQLLLSAAVTAGKIAIDRGYDIAQISRHLDFISLLTYDFHGAWRQTVGHHSPLFRGNEDASSRFSNADYAVSYMLRLGAPANKLVMGIPTFGRSYTLASSKTDVGAPISGPGIPGRFTKWKGILAYYEICDFLHGATTHRFRDQQVPYATKGNQWVAYDDQESVKNKARYLKNRQLAGAMVWALDLDDFRGTFCGQNLTFPLTSAIKDVLARV 362
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210|      221       231       241       251       261       271       281       291       301       311       321       331       341       351       361 
                                                                                                                                                                                                                                           210|                                                                                                                                                      
                                                                                                                                                                                                                                            212
   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 4ML4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ML4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ML4)

(-) Gene Ontology  (25, 25)

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
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PYE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:119 - Trp A:120   [ RasMol ]  
    Ser A:36 - Phe A:37   [ RasMol ]  
    Trp A:331 - Ala A:332   [ 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
  4ml4
    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
  CH3L1_BUBBU | Q7YS85
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  CH3L1_BUBBU | Q7YS85
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CH3L1_BUBBU | Q7YS85: 1tfv 2o9o 2qf8 4mav 4mpk 4mtv 4nsb 4q7n 4s06 5wsi 5wsj 5wsm

(-) Related Entries Specified in the PDB File

2o9o