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(-) Description

Title :  CRYSTAL STRUCTURE OF (PRO-PRO-GLY)9 AT 1.1 A RESOLUTION
 
Authors :  K. Okuyama, T. Morimoto, C. Hongo, N. Hosaka, N. Nishino
Date :  22 Apr 10  (Deposition) - 06 Apr 11  (Release) - 06 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.08
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Collagen, Triple Helix, Model Peptide, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Okuyama, T. Morimoto, C. Hongo, N. Hosaka, N. Nishino
Crystal Structure Of (Pro-Pro-Gly)9
To Be Published
PubMed: search

(-) Compounds

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

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2AZI4Ligand/IonAZIDE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ACY-1Ligand/IonACETIC ACID
2AZI2Ligand/IonAZIDE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2AZI2Ligand/IonAZIDE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO B:13 , HOH B:434 , HOH B:442 , HOH B:627 , HOH F:417BINDING SITE FOR RESIDUE AZI B 103
2AC2SOFTWAREPRO C:7 , HOH C:522BINDING SITE FOR RESIDUE AZI C 104
3AC3SOFTWAREPRO A:11 , HOH D:647BINDING SITE FOR RESIDUE AZI D 102
4AC4SOFTWAREPRO B:17 , HOH E:648BINDING SITE FOR RESIDUE AZI E 101
5AC5SOFTWAREHOH D:556 , PRO E:10 , HOH E:578BINDING SITE FOR RESIDUE ACY E 201
6AC6SOFTWAREPRO E:17 , HOH E:548 , HOH E:552 , HOH E:595 , PRO F:19BINDING SITE FOR RESIDUE ACY E 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3AH9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3AH9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3AH9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3AH9)

(-) Exons   (0, 0)

(no "Exon" information available for 3AH9)

(-) 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:24
 aligned with Q80BK4_SHV2 | Q80BK4 from UniProtKB/TrEMBL  Length:99

    Alignment length:24
                                    50        60    
           Q80BK4_SHV2   41 PGPPGPPGPPGPPGPPGPPGPPGP 64
               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
                  3ah9 A  2 PGPPGPPGPPGPPGPPGPPGPPGP 25
                                    11        21    


Chain B from PDB  Type:PROTEIN  Length:25
 aligned with Q80BK4_SHV2 | Q80BK4 from UniProtKB/TrEMBL  Length:99

    Alignment length:25
                                    49        59     
           Q80BK4_SHV2   40 PPGPPGPPGPPGPPGPPGPPGPPGP 64
               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
                  3ah9 B  1 PPGPPGPPGPPGPPGPPGPPGPPGP 25
                                    10        20     


Chain C from PDB  Type:PROTEIN  Length:25
 aligned with Q80BK4_SHV2 | Q80BK4 from UniProtKB/TrEMBL  Length:99

    Alignment length:25
                                    49        59     
           Q80BK4_SHV2   40 PPGPPGPPGPPGPPGPPGPPGPPGP 64
               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
                  3ah9 C  1 PPGPPGPPGPPGPPGPPGPPGPPGP 25
                                    10        20     


Chain D from PDB  Type:PROTEIN  Length:22
 aligned with Q80BK4_SHV2 | Q80BK4 from UniProtKB/TrEMBL  Length:99

    Alignment length:22
                                    54        64  
           Q80BK4_SHV2   45 GPPGPPGPPGPPGPPGPPGPPG 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
                  3ah9 D  3 GPPGPPGPPGPPGPPGPPGPPG 24
                                    12        22  


Chain E from PDB  Type:PROTEIN  Length:25
 aligned with Q80BK4_SHV2 | Q80BK4 from UniProtKB/TrEMBL  Length:99

    Alignment length:25
                                    49        59     
           Q80BK4_SHV2   40 PPGPPGPPGPPGPPGPPGPPGPPGP 64
               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
                  3ah9 E  1 PPGPPGPPGPPGPPGPPGPPGPPGP 25
                                    10        20     


Chain F from PDB  Type:PROTEIN  Length:24
 aligned with Q80BK4_SHV2 | Q80BK4 from UniProtKB/TrEMBL  Length:99

    Alignment length:24
                                    52        62    
           Q80BK4_SHV2   43 PPGPPGPPGPPGPPGPPGPPGPPG 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
                  3ah9 F  4 PPGPPGPPGPPGPPGPPGPPGPPG 27
                                    13        23
   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 3AH9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3AH9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AH9)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (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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  3ah9
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  Q80BK4_SHV2 | Q80BK4
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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 3ai6 3b0s 3b2c

(-) Related Entries Specified in the PDB File

1k6f THE COLLAGEN-LIKE PEPTIDE WITH THE SAME SEQUENCE AND LONGER CHAIN LENGTH.
1v4f THE COLLAGEN-LIKE PEPTIDE WITH GLY-PRO-HYP SEQUENCE.
2cuo THE SAME COLLAGEN-LIKE PEPTIDE. ITS STRUCTURE WAS ANALYZED AGAINST THE TWINNED DIFFRACTION DATA.