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(-) Description

Title :  STRUCTURE OF (PPG)4-OOG-(PPG)4, MONOCLINIC, TWINNED CRYSTAL
 
Authors :  K. Okuyama, T. Morimoto, G. Wu, K. Noguchi, K. Mizuno, H. P. Bachinger
Date :  06 Mar 09  (Deposition) - 12 Jan 10  (Release) - 17 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.22
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Biol. Unit 3:  A,B,C,D,E,F  (1x)
Keywords :  Collagen Helix, Host-Guest Peptide, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Okuyama, T. Morimoto, H. Narita, T. Kawaguchi, K. Mizuno, H. P. Bachinger, G. Wu, K. Noguchi
Two Crystal Modifications Of (Pro-Pro-Gly)4-Hyp-Hyp-Gly-(Pro-Pro-Gly)4 Reveal The Puckering Preference Of Hyp(X) In The Hyp(X):Hyp(Y) And Hyp(X):Pro(Y) Stacking Pairs In Collagen Helices.
Acta Crystallogr. , Sect. D V. 66 88 2010
PubMed-ID: 20057053  |  Reference-DOI: 10.1107/S0907444909046642

(-) Compounds

Molecule 1 - COLLAGEN-LIKE PEPTIDE
    Chains: A, B, C, D, E, F
    Engineered: YES
    Other Details: THIS PEPTIDE WAS CHEMICALLY SYSTHESIZED.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF
Biological Unit 3 (1x): ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric Unit (1, 12)
No.NameCountTypeFull Name
1HYP12Mod. Amino Acid4-HYDROXYPROLINE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1HYP6Mod. Amino Acid4-HYDROXYPROLINE
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1HYP6Mod. Amino Acid4-HYDROXYPROLINE
Biological Unit 3 (1, 12)
No.NameCountTypeFull Name
1HYP12Mod. Amino Acid4-HYDROXYPROLINE

(-) Sites  (0, 0)

(no "Site" information available for 3A08)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3A08)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3A08)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3A08)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3A08)

(-) Exons   (0, 0)

(no "Exon" information available for 3A08)

(-) 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:23
                                                      
               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
                  3a08 A  1 PPGPPGPPGPPGppGPPGPPGPP 23
                                    10  ||    20   
                                       13-HYP      
                                        14-HYP     


Chain B from PDB  Type:PROTEIN  Length:23
                                                      
               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
                  3a08 B  1 PPGPPGPPGPPGppGPPGPPGPP 23
                                    10  ||    20   
                                       13-HYP      
                                        14-HYP     


Chain C from PDB  Type:PROTEIN  Length:23
                                                      
               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
                  3a08 C  3 GPPGPPGPPGppGPPGPPGPPGP 25
                                    12||      22   
                                     13-HYP        
                                      14-HYP       


Chain D from PDB  Type:PROTEIN  Length:25
                                                        
               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
                  3a08 D  3 GPPGPPGPPGppGPPGPPGPPGPPG 27
                                    12||      22     
                                     13-HYP          
                                      14-HYP         


Chain E from PDB  Type:PROTEIN  Length:24
                                                       
               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
                  3a08 E  3 GPPGPPGPPGppGPPGPPGPPGPP 26
                                    12||      22    
                                     13-HYP         
                                      14-HYP        


Chain F from PDB  Type:PROTEIN  Length:23
                                                      
               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
                  3a08 F  5 PGPPGPPGppGPPGPPGPPGPPG 27
                                    14        24   
                                   13-HYP          
                                    14-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 3A08)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3A08)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3A08)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3A08)

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  3a08
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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1x1k THE RELATED HOST-GUEST PEPTIDE
2cuo THE SIMILAR COLLAGEN-LIKE PEPTIDE.
2d3f THE RELATED HOST-GUEST PEPTIDE.
2d3h THE STRUCTURE WAS REFINED AGAINST THE SAME INTENSITIES WITH THE TWINNED DATA.