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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COLLAGEN TRIPLE HELIX MODEL [{PRO-HYP(R)-GLY}4-{HYP(S)-PRO-GLY}2-{PRO-HYP(R)-GLY}4]3
 
Authors :  D. Motooka, K. Kawahara, S. Nakamura, M. Doi, Y. Nishi, Y. Nishiuchi, T. T. Yoshida, T. Ohkubo, Y. Kobayashi, Y. K. Kang, S. Uchiyama
Date :  26 Jul 11  (Deposition) - 04 Apr 12  (Release) - 04 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.36
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Biol. Unit 3:  G,H,I  (1x)
Keywords :  Collagen Stability, Puckering, Amino Acid-Preferences, Triple Helix, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Motooka, K. Kawahara, S. Nakamura, M. Doi, Y. Nishi, Y. Nishiuchi, Y. Kee Kang, T. Nakazawa, S. Uchiyama, T. Yoshida, T. Ohkubo, Y. Kobayashi
The Triple Helical Structure And Stability Of Collagen Mode Peptide With 4(S)-Hydroxyprolyl-Pro-Gly Units
Biopolymers V. 98 111 2011
PubMed-ID: 22020801  |  Reference-DOI: 10.1002/BIP.21730

(-) Compounds

Molecule 1 - COLLAGEN-LIKE PEPTIDE
    Chains: A, B, C, D, E, F, G, H, I
    Engineered: YES
    Other Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789
Asymmetric Unit : ABCDEFGHI
Biological Unit 1 (1x): ABC      
Biological Unit 2 (1x):    DEF   
Biological Unit 3 (1x):       GHI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 90)

Asymmetric Unit (2, 90)
No.NameCountTypeFull Name
1HYP72Mod. Amino Acid4-HYDROXYPROLINE
2HZP18Mod. Amino Acid(4S)-4-HYDROXY-L-PROLINE
Biological Unit 1 (2, 30)
No.NameCountTypeFull Name
1HYP24Mod. Amino Acid4-HYDROXYPROLINE
2HZP6Mod. Amino Acid(4S)-4-HYDROXY-L-PROLINE
Biological Unit 2 (2, 30)
No.NameCountTypeFull Name
1HYP24Mod. Amino Acid4-HYDROXYPROLINE
2HZP6Mod. Amino Acid(4S)-4-HYDROXY-L-PROLINE
Biological Unit 3 (2, 30)
No.NameCountTypeFull Name
1HYP24Mod. Amino Acid4-HYDROXYPROLINE
2HZP6Mod. Amino Acid(4S)-4-HYDROXY-L-PROLINE

(-) Sites  (0, 0)

(no "Site" information available for 3B2C)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3B2C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3B2C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3B2C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3B2C)

(-) Exons   (0, 0)

(no "Exon" information available for 3B2C)

(-) 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:30
 aligned with Q80BK4_SHV2 | Q80BK4 from UniProtKB/TrEMBL  Length:99

    Alignment length:30
                                    46        56        66
           Q80BK4_SHV2   37 PPGPPGPPGPPGPPGPPGPPGPPGPPGPPG 66
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .............................. Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                  3b2c A  1 PpGPpGPpGPpGpPGpPGPpGPpGPpGPpG 30
                             |  |  |10| |  |  20  |  |  30
                             |  |  |  | |  |   |  |  |  | 
                             2-HYP |  | |  |   |  |  |  | 
                                5-HYP | |  |   |  |  |  | 
                                   8-HYP|  |   |  |  |  | 
                                     11-HYP|   |  |  |  | 
                                       13-HZP  |  |  |  | 
                                          16-HZP  |  |  | 
                                              20-HYP |  | 
                                                 23-HYP | 


Chain B from PDB  Type:PROTEIN  Length:30
 aligned with Q80BK4_SHV2 | Q80BK4 from UniProtKB/TrEMBL  Length:99

    Alignment length:30
                                    46        56        66
           Q80BK4_SHV2   37 PPGPPGPPGPPGPPGPPGPPGPPGPPGPPG 66
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .............................. Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                  3b2c B  1 PpGPpGPpGPpGpPGpPGPpGPpGPpGPpG 30
                             |  |  |10| |  |  20  |  |  30
                             |  |  |  | |  |   |  |  |  | 
                             2-HYP |  | |  |   |  |  |  | 
                                5-HYP | |  |   |  |  |  | 
                                   8-HYP|  |   |  |  |  | 
                                     11-HYP|   |  |  |  | 
                                       13-HZP  |  |  |  | 
                                          16-HZP  |  |  | 
                                              20-HYP |  | 
                                                 23-HYP | 


Chain C from PDB  Type:PROTEIN  Length:30
 aligned with Q80BK4_SHV2 | Q80BK4 from UniProtKB/TrEMBL  Length:99

    Alignment length:30
                                    46        56        66
           Q80BK4_SHV2   37 PPGPPGPPGPPGPPGPPGPPGPPGPPGPPG 66
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .............................. Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                  3b2c C  1 PpGPpGPpGPpGpPGpPGPpGPpGPpGPpG 30
                             |  |  |10| |  |  20  |  |  30
                             |  |  |  | |  |   |  |  |  | 
                             2-HYP |  | |  |   |  |  |  | 
                                5-HYP | |  |   |  |  |  | 
                                   8-HYP|  |   |  |  |  | 
                                     11-HYP|   |  |  |  | 
                                       13-HZP  |  |  |  | 
                                          16-HZP  |  |  | 
                                              20-HYP |  | 
                                                 23-HYP | 


Chain D from PDB  Type:PROTEIN  Length:30
 aligned with Q80BK4_SHV2 | Q80BK4 from UniProtKB/TrEMBL  Length:99

    Alignment length:30
                                    46        56        66
           Q80BK4_SHV2   37 PPGPPGPPGPPGPPGPPGPPGPPGPPGPPG 66
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .............................. Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                  3b2c D  1 PpGPpGPpGPpGpPGpPGPpGPpGPpGPpG 30
                             |  |  |10| |  |  20  |  |  30
                             |  |  |  | |  |   |  |  |  | 
                             2-HYP |  | |  |   |  |  |  | 
                                5-HYP | |  |   |  |  |  | 
                                   8-HYP|  |   |  |  |  | 
                                     11-HYP|   |  |  |  | 
                                       13-HZP  |  |  |  | 
                                          16-HZP  |  |  | 
                                              20-HYP |  | 
                                                 23-HYP | 


Chain E from PDB  Type:PROTEIN  Length:30
 aligned with Q80BK4_SHV2 | Q80BK4 from UniProtKB/TrEMBL  Length:99

    Alignment length:30
                                    46        56        66
           Q80BK4_SHV2   37 PPGPPGPPGPPGPPGPPGPPGPPGPPGPPG 66
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .............................. Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                  3b2c E  1 PpGPpGPpGPpGpPGpPGPpGPpGPpGPpG 30
                             |  |  |10| |  |  20  |  |  30
                             |  |  |  | |  |   |  |  |  | 
                             2-HYP |  | |  |   |  |  |  | 
                                5-HYP | |  |   |  |  |  | 
                                   8-HYP|  |   |  |  |  | 
                                     11-HYP|   |  |  |  | 
                                       13-HZP  |  |  |  | 
                                          16-HZP  |  |  | 
                                              20-HYP |  | 
                                                 23-HYP | 


Chain F from PDB  Type:PROTEIN  Length:30
 aligned with Q80BK4_SHV2 | Q80BK4 from UniProtKB/TrEMBL  Length:99

    Alignment length:30
                                    46        56        66
           Q80BK4_SHV2   37 PPGPPGPPGPPGPPGPPGPPGPPGPPGPPG 66
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .............................. Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                  3b2c F  1 PpGPpGPpGPpGpPGpPGPpGPpGPpGPpG 30
                             |  |  |10| |  |  20  |  |  30
                             |  |  |  | |  |   |  |  |  | 
                             2-HYP |  | |  |   |  |  |  | 
                                5-HYP | |  |   |  |  |  | 
                                   8-HYP|  |   |  |  |  | 
                                     11-HYP|   |  |  |  | 
                                       13-HZP  |  |  |  | 
                                          16-HZP  |  |  | 
                                              20-HYP |  | 
                                                 23-HYP | 


Chain G from PDB  Type:PROTEIN  Length:30
 aligned with Q80BK4_SHV2 | Q80BK4 from UniProtKB/TrEMBL  Length:99

    Alignment length:30
                                    46        56        66
           Q80BK4_SHV2   37 PPGPPGPPGPPGPPGPPGPPGPPGPPGPPG 66
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .............................. Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                  3b2c G  1 PpGPpGPpGPpGpPGpPGPpGPpGPpGPpG 30
                             |  |  |10| |  |  20  |  |  30
                             |  |  |  | |  |   |  |  |  | 
                             2-HYP |  | |  |   |  |  |  | 
                                5-HYP | |  |   |  |  |  | 
                                   8-HYP|  |   |  |  |  | 
                                     11-HYP|   |  |  |  | 
                                       13-HZP  |  |  |  | 
                                          16-HZP  |  |  | 
                                              20-HYP |  | 
                                                 23-HYP | 


Chain H from PDB  Type:PROTEIN  Length:30
 aligned with Q80BK4_SHV2 | Q80BK4 from UniProtKB/TrEMBL  Length:99

    Alignment length:30
                                    46        56        66
           Q80BK4_SHV2   37 PPGPPGPPGPPGPPGPPGPPGPPGPPGPPG 66
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .............................. Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                  3b2c H  1 PpGPpGPpGPpGpPGpPGPpGPpGPpGPpG 30
                             |  |  |10| |  |  20  |  |  30
                             |  |  |  | |  |   |  |  |  | 
                             2-HYP |  | |  |   |  |  |  | 
                                5-HYP | |  |   |  |  |  | 
                                   8-HYP|  |   |  |  |  | 
                                     11-HYP|   |  |  |  | 
                                       13-HZP  |  |  |  | 
                                          16-HZP  |  |  | 
                                              20-HYP |  | 
                                                 23-HYP | 


Chain I from PDB  Type:PROTEIN  Length:30
 aligned with Q80BK4_SHV2 | Q80BK4 from UniProtKB/TrEMBL  Length:99

    Alignment length:30
                                    46        56        66
           Q80BK4_SHV2   37 PPGPPGPPGPPGPPGPPGPPGPPGPPGPPG 66
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .............................. Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                  3b2c I  1 PpGPpGPpGPpGpPGpPGPpGPpGPpGPpG 30
                             |  |  |10| |  |  20  |  |  30
                             |  |  |  | |  |   |  |  |  | 
                             2-HYP |  | |  |   |  |  |  | 
                                5-HYP | |  |   |  |  |  | 
                                   8-HYP|  |   |  |  |  | 
                                     11-HYP|   |  |  |  | 
                                       13-HZP  |  |  |  | 
                                          16-HZP  |  |  | 
                                              20-HYP |  | 
                                                 23-HYP |
   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 3B2C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3B2C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3B2C)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H,I   (Q80BK4_SHV2 | Q80BK4)
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/TrEMBL
        Q80BK4_SHV2 | Q80BK4: 1k6f 1wzb 1x1k 1ym8 2cuo 2d3f 2d3h 3ah9 3ai6 3b0s

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3B2C)