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 TYPE IX COLLAGEN NC2 HETERO-TRIMERIZATION DOMAIN WITH A GUEST FRAGMENT A2A1A1 OF TYPE I COLLAGEN (NATIVE FORM)
 
Authors :  S. P. Boudko, H. P. Bachinger
Date :  24 Jul 15  (Deposition) - 03 Aug 16  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Collagen, Hetero-Trimerization, Chain Stagger, Chain Register, Triple Helix, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. P. Boudko, H. P. Bachinger
Structural Insight For Chain Selection And Stagger Control In Collagen.
Sci Rep V. 6 37831 2016
PubMed-ID: 27897211  |  Reference-DOI: 10.1038/SREP37831

(-) Compounds

Molecule 1 - COLLAGEN ALPHA-1(I) CHAIN,COLLAGEN ALPHA-1(IX) CHAIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 572-583,UNP RESIDUES 754-789
    Gene: COL1A1, COL9A1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ALPHA-1 TYPE I COLLAGEN
 
Molecule 2 - COLLAGEN ALPHA-2(I) CHAIN,COLLAGEN ALPHA-2(IX) CHAIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 484-495,UNP RESIDUES 517-552
    Gene: COL1A2, COL9A2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ALPHA-2 TYPE I COLLAGEN
 
Molecule 3 - COLLAGEN ALPHA-1(I) CHAIN,COLLAGEN ALPHA-3(IX) CHAIN
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 572-583,UNP RESIDUES 517-553
    Gene: COL1A1, COL9A3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ALPHA-1 TYPE I COLLAGEN

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:42 , ASN B:22 , ILE B:23 , ASP B:46 , LEU B:49 , GLN B:53binding site for residue GOL B 101
2AC2SOFTWAREPHE A:25 , HOH A:106 , MET C:51 , GLU C:54 , GLN C:55 , GLN C:58binding site for residue GOL C 101
3AC3SOFTWAREPRO A:26 , GLY A:27 , PHE A:56 , GLN C:55 , GLN C:58 , LEU C:59 , HIS C:62binding site for residue GOL C 102

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:48 -C:48

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5CTI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CTI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CTI)

(-) Exons   (0, 0)

(no "Exon" information available for 5CTI)

(-) 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:66
                                                                                                 
               SCOP domains ------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......................................hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  5cti A  2 SGPPGPPGPPGPPGARGQAGVMGFPGPPGPPGPPGRAPTDQHIKQVCMRVIQEHFAEMAASLKRPD 67
                                    11        21        31        41        51        61      


Chain B from PDB  Type:PROTEIN  Length:71
                                                                                                      
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  5cti B  1 GSGPPGPPGPPGPPGARGEPGNIGFPGPPGPPGPPGRDATDQHIVDVALKMLQEQLAEVAVSAKREALGAV 71
                                    10        20        30        40        50        60        70 


Chain C from PDB  Type:PROTEIN  Length:71
                                                                                                      
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................................hhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  5cti C  2 SGPPGPPGPPGPPGARGQAGVMGFPGPPGPPGPPGKEASEQRIRELCGGMISEQIAQLAAHLRKPLAPGSI 72
                                    11        21        31        41        51        61        71
   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 5CTI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CTI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CTI)

(-) Gene Ontology  (84, 129)

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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5cti)
 

(-) 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
  5cti
    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
  CO1A1_HUMAN | P02452
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  CO1A2_HUMAN | P08123
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  CO9A1_HUMAN | P20849
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  CO9A2_HUMAN | Q14055
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  CO9A3_HUMAN | Q14050
    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
  CO1A1_HUMAN | P02452
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  CO1A2_HUMAN | P08123
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  CO9A1_HUMAN | P20849
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  CO9A2_HUMAN | Q14055
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  CO9A3_HUMAN | Q14050
    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
        CO1A1_HUMAN | P02452: 1q7d 2llp 3ejh 3gxe 5ctd 5cva 5cvb 5k31
        CO1A2_HUMAN | P08123: 5ctd 5cva
        CO9A1_HUMAN | P20849: 2uur 5ctd 5cva 5cvb
        CO9A2_HUMAN | Q14055: 5ctd 5cva 5cvb
        CO9A3_HUMAN | Q14050: 5ctd 5cva 5cvb

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5CTI)