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

(-) Description

Title :  CHONDROITIN-4-SULFATE. THE STRUCTURE OF A SULFATED GLYCOSAMINOGLYCAN
 
Authors :  S. Arnott
Date :  23 May 78  (Deposition) - 28 Mar 80  (Release) - 25 Aug 09  (Revision)
Method :  FIBER DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A
Keywords :  Texture Of Connective Tissue (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. T. Winter, S. Arnott, D. H. Isaac, E. D. Atkins
Chondroitin 4-Sulfate: The Structure Of A Sulfated Glycosaminoglycan.
J. Mol. Biol. V. 125 1 1978
PubMed-ID: 712855  |  Reference-DOI: 10.1016/0022-2836(78)90251-6
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SUGAR (12-MER)
    Chains: A
    Engineered: YES
    Organism Common: BOVINE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Tissue: NASAL SEPTA

 Structural Features

(-) Chains, Units

  
Asymmetric Unit : 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
1ASG3OTHER2-DEOXY-2-ACETAMIDO-BETA-D-GALACTOSE-4-SULFATE
2GC42OTHER4-DEOXY-D-GLUCURONIC ACID
3GCU1OTHERD-GLUCURONIC ACID
4NA6Ligand/IonSODIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASG A:2 , GCU A:3 , ASG A:4 , GC4 A:5 , ASG A:6 , HOH A:8 , HOH A:18 , HOH A:28BINDING SITE FOR RESIDUE GC4 A 1
02AC2SOFTWAREGC4 A:1 , GCU A:3 , ASG A:4 , GC4 A:5 , ASG A:6 , HOH A:8 , HOH A:10 , HOH A:11 , HOH A:12 , HOH A:13 , HOH A:15 , HOH A:16 , HOH A:18 , HOH A:20 , HOH A:21 , HOH A:22 , HOH A:23 , HOH A:25 , HOH A:26 , HOH A:28 , HOH A:30 , HOH A:31 , HOH A:32 , HOH A:33 , HOH A:35 , HOH A:36 , NA A:40 , NA A:41 , NA A:42 , NA A:43 , NA A:44 , NA A:45BINDING SITE FOR RESIDUE ASG A 2
03AC3SOFTWAREGC4 A:1 , ASG A:2 , ASG A:4 , GC4 A:5 , ASG A:6 , HOH A:8 , HOH A:18 , HOH A:28BINDING SITE FOR RESIDUE GCU A 3
04AC4SOFTWAREGC4 A:1 , ASG A:2 , GCU A:3 , GC4 A:5 , ASG A:6 , HOH A:8 , HOH A:10 , HOH A:11 , HOH A:12 , HOH A:13 , HOH A:15 , HOH A:16 , HOH A:18 , HOH A:20 , HOH A:21 , HOH A:22 , HOH A:23 , HOH A:25 , HOH A:26 , HOH A:28 , HOH A:30 , HOH A:31 , HOH A:32 , HOH A:33 , HOH A:35 , HOH A:36 , NA A:40 , NA A:41 , NA A:42 , NA A:43 , NA A:44 , NA A:45BINDING SITE FOR RESIDUE ASG A 4
05AC5SOFTWAREGC4 A:1 , ASG A:2 , GCU A:3 , ASG A:4 , ASG A:6 , HOH A:8 , HOH A:18 , HOH A:28BINDING SITE FOR RESIDUE GC4 A 5
06AC6SOFTWAREGC4 A:1 , ASG A:2 , GCU A:3 , ASG A:4 , GC4 A:5 , HOH A:8 , HOH A:10 , HOH A:11 , HOH A:12 , HOH A:13 , HOH A:15 , HOH A:16 , HOH A:18 , HOH A:20 , HOH A:21 , HOH A:22 , HOH A:23 , HOH A:25 , HOH A:26 , HOH A:28 , HOH A:30 , HOH A:31 , HOH A:32 , HOH A:33 , HOH A:35 , HOH A:36 , NA A:40 , NA A:41 , NA A:42 , NA A:43 , NA A:44 , NA A:45BINDING SITE FOR RESIDUE ASG A 6
07AC7SOFTWAREASG A:2 , ASG A:4 , ASG A:6 , HOH A:7 , HOH A:8 , HOH A:9 , HOH A:10 , HOH A:11 , HOH A:17 , HOH A:18 , HOH A:19 , HOH A:20 , HOH A:21 , HOH A:27 , HOH A:28 , HOH A:29 , HOH A:30 , HOH A:31BINDING SITE FOR RESIDUE NA A 40
08AC8SOFTWAREASG A:2 , ASG A:4 , ASG A:6 , HOH A:11 , HOH A:12 , HOH A:13 , HOH A:14 , HOH A:15 , HOH A:16 , HOH A:21 , HOH A:22 , HOH A:23 , HOH A:24 , HOH A:25 , HOH A:26 , HOH A:31 , HOH A:32 , HOH A:33 , HOH A:34 , HOH A:35 , HOH A:36BINDING SITE FOR RESIDUE NA A 41
09AC9SOFTWAREASG A:2 , ASG A:4 , ASG A:6 , HOH A:7 , HOH A:8 , HOH A:9 , HOH A:10 , HOH A:11 , HOH A:17 , HOH A:18 , HOH A:19 , HOH A:20 , HOH A:21 , HOH A:27 , HOH A:28 , HOH A:29 , HOH A:30 , HOH A:31BINDING SITE FOR RESIDUE NA A 42
10BC1SOFTWAREASG A:2 , ASG A:4 , ASG A:6 , HOH A:11 , HOH A:12 , HOH A:13 , HOH A:14 , HOH A:15 , HOH A:16 , HOH A:21 , HOH A:22 , HOH A:23 , HOH A:24 , HOH A:25 , HOH A:26 , HOH A:31 , HOH A:32 , HOH A:33 , HOH A:34 , HOH A:35 , HOH A:36BINDING SITE FOR RESIDUE NA A 43
11BC2SOFTWAREASG A:2 , ASG A:4 , ASG A:6 , HOH A:7 , HOH A:8 , HOH A:9 , HOH A:10 , HOH A:11 , HOH A:17 , HOH A:18 , HOH A:19 , HOH A:20 , HOH A:21 , HOH A:27 , HOH A:28 , HOH A:29 , HOH A:30 , HOH A:31BINDING SITE FOR RESIDUE NA A 44
12BC3SOFTWAREASG A:2 , ASG A:4 , ASG A:6 , HOH A:11 , HOH A:12 , HOH A:13 , HOH A:14 , HOH A:15 , HOH A:16 , HOH A:21 , HOH A:22 , HOH A:23 , HOH A:24 , HOH A:25 , HOH A:26 , HOH A:31 , HOH A:32 , HOH A:33 , HOH A:34 , HOH A:35 , HOH A:36BINDING SITE FOR RESIDUE NA A 45

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1C4S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1C4S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1C4S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1C4S)

(-) Exons   (0, 0)

(no "Exon" information available for 1C4S)

(-) 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:OTHER  Length:6
                                    
                   1c4s A 1 xxxxxx 6
                            ||||||
                            ||||||
                            1-GC4|
                             2-ASG
                              3-GCU
                               4-ASG
                                5-GC4
                                 6-ASG
   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 1C4S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1C4S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1C4S)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1C4S)

 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
    ASG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GC4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GCU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ 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 ]
    BC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1c4s)
 

(-) 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 ](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)
Insightii
  sticks, numbering, Na+: spacefill, no water
[ mono GIF format | stereo GIF format ]
  spacefill, Na+, no water
[ mono GIF format | stereo GIF format ]
  spacefill, Na+, water
[ mono GIF format | stereo GIF format ]

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1c4s
    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 | HSSP
    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
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
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
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1C4S)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1C4S)