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(-) Description

Title :  AN ALPHA/BETA-PEPTIDE HELIX BUNDLE WITH A PURE BETA-AMINO ACID CORE AND A DISTINCTIVE QUARTERNARY STRUCTURE: GCN4PLI DERIVATIVE WITH BETA RESIDUES AT A AND D HEPTAD POSITIONS - HIGHER SYMMETRY CRYSTAL
 
Authors :  M. W. Giuliano, W. S. Horne, S. H. Gellman
Date :  11 Nov 08  (Deposition) - 21 Jul 09  (Release) - 18 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  C,D  (2x)
Keywords :  Alpha/Beta-Peptide, Helix Bundle, Foldamer, Coiled Coil, Gcn4 Derivative, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. W. Giuliano, W. S. Horne, S. H. Gellman
An Alpha/Beta-Peptide Helix Bundle With A Pure Beta3-Amino Acid Core And A Distinctive Quaternary Structure.
J. Am. Chem. Soc. V. 131 9860 2009
PubMed-ID: 19580264  |  Reference-DOI: 10.1021/JA8099294
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GCN4PLI-BETAAD
    Chains: A, B, C, D
    Engineered: YES
    Other Details: A HYBRID ALPHA/BETA PEPTIDE BASED ON THE GCN4PLI SEQUENCE, A AND D HEPTAD POSITIONS ARE SUBSTITUTED WITH BETA-3-AMINO ACIDS. THIS WAS CRYSTALLIZED FROM AN IODIDE-CONTAINING BUFFER.
    Other Details - Source: SYNTHETIC PEPTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): AB  
Biological Unit 2 (2x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 53)

Asymmetric Unit (6, 53)
No.NameCountTypeFull Name
1ACE4Mod. Amino AcidACETYL GROUP
2B3L16Mod. Amino Acid(3S)-3-AMINO-5-METHYLHEXANOIC ACID
3B3M4Mod. Amino Acid(3R)-3-AMINO-5-(METHYLSULFANYL)PENTANOIC ACID
4BIL16Mod. Amino Acid(3R,4S)-3-AMINO-4-METHYLHEXANOIC ACID
5HMR4Mod. Amino AcidBETA-HOMOARGININE
6IOD9Ligand/IonIODIDE ION
Biological Unit 1 (6, 58)
No.NameCountTypeFull Name
1ACE4Mod. Amino AcidACETYL GROUP
2B3L16Mod. Amino Acid(3S)-3-AMINO-5-METHYLHEXANOIC ACID
3B3M4Mod. Amino Acid(3R)-3-AMINO-5-(METHYLSULFANYL)PENTANOIC ACID
4BIL16Mod. Amino Acid(3R,4S)-3-AMINO-4-METHYLHEXANOIC ACID
5HMR4Mod. Amino AcidBETA-HOMOARGININE
6IOD14Ligand/IonIODIDE ION
Biological Unit 2 (6, 48)
No.NameCountTypeFull Name
1ACE4Mod. Amino AcidACETYL GROUP
2B3L16Mod. Amino Acid(3S)-3-AMINO-5-METHYLHEXANOIC ACID
3B3M4Mod. Amino Acid(3R)-3-AMINO-5-(METHYLSULFANYL)PENTANOIC ACID
4BIL16Mod. Amino Acid(3R,4S)-3-AMINO-4-METHYLHEXANOIC ACID
5HMR4Mod. Amino AcidBETA-HOMOARGININE
6IOD4Ligand/IonIODIDE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREBIL A:5 , ARG B:25BINDING SITE FOR RESIDUE IOD A 34
2AC2SOFTWARELYS A:15 , IOD A:36BINDING SITE FOR RESIDUE IOD A 35
3AC3SOFTWAREHIS A:18 , IOD A:35 , LYS B:15BINDING SITE FOR RESIDUE IOD A 36
4AC4SOFTWAREHOH D:37BINDING SITE FOR RESIDUE IOD B 34
5AC5SOFTWAREHMR B:33BINDING SITE FOR RESIDUE IOD B 35
6AC6SOFTWAREGLU B:10 , LYS C:15BINDING SITE FOR RESIDUE IOD C 34
7AC7SOFTWAREHIS C:18 , BIL C:19 , LYS D:15BINDING SITE FOR RESIDUE IOD C 35

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F87)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3F87)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3F87)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3F87)

(-) Exons   (0, 0)

(no "Exon" information available for 3F87)

(-) 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:34
                                                                 
               SCOP domains ---------------------------------- SCOP domains
               CATH domains ---------------------------------- CATH domains
               Pfam domains ---------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------- PROSITE
                 Transcript ---------------------------------- Transcript
                  3f87 A  0 xRxKQxEDKxEExLSKxYHxENExARxKKLxGEr 33
                            | |  |   9  |   | 19   |  | 29|  |
                            | |  |   |  |   |  |   |  |   |  |
                            0-ACE|   |  |   |  |   |  |   |  |
                              2-B3M  |  |   |  |   |  |   |  |
                                 5-BIL  |   |  |   |  |   |  |
                                     9-B3L  |  |   |  |   |  |
                                       12-BIL  |   |  |   |  |
                                           16-B3L  |  |   |  |
                                              19-BIL  |   |  |
                                                  23-B3L  |  |


Chain B from PDB  Type:PROTEIN  Length:34
                                                                 
               SCOP domains ---------------------------------- SCOP domains
               CATH domains ---------------------------------- CATH domains
               Pfam domains ---------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------- PROSITE
                 Transcript ---------------------------------- Transcript
                  3f87 B  0 xRxKQxEDKxEExLSKxYHxENExARxKKLxGEr 33
                            | |  |   9  |   | 19   |  | 29|  |
                            | |  |   |  |   |  |   |  |   |  |
                            0-ACE|   |  |   |  |   |  |   |  |
                              2-B3M  |  |   |  |   |  |   |  |
                                 5-BIL  |   |  |   |  |   |  |
                                     9-B3L  |  |   |  |   |  |
                                       12-BIL  |   |  |   |  |
                                           16-B3L  |  |   |  |
                                              19-BIL  |   |  |
                                                  23-B3L  |  |


Chain C from PDB  Type:PROTEIN  Length:34
                                                                 
               SCOP domains ---------------------------------- SCOP domains
               CATH domains ---------------------------------- CATH domains
               Pfam domains ---------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------- PROSITE
                 Transcript ---------------------------------- Transcript
                  3f87 C  0 xRxKQxEDKxEExLSKxYHxENExARxKKLxGEr 33
                            | |  |   9  |   | 19   |  | 29|  |
                            | |  |   |  |   |  |   |  |   |  |
                            0-ACE|   |  |   |  |   |  |   |  |
                              2-B3M  |  |   |  |   |  |   |  |
                                 5-BIL  |   |  |   |  |   |  |
                                     9-B3L  |  |   |  |   |  |
                                       12-BIL  |   |  |   |  |
                                           16-B3L  |  |   |  |
                                              19-BIL  |   |  |
                                                  23-B3L  |  |


Chain D from PDB  Type:PROTEIN  Length:34
                                                                 
               SCOP domains ---------------------------------- SCOP domains
               CATH domains ---------------------------------- CATH domains
               Pfam domains ---------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------- PROSITE
                 Transcript ---------------------------------- Transcript
                  3f87 D  0 xRxKQxEDKxEExLSKxYHxENExARxKKLxGEr 33
                            | |  |   9  |   | 19   |  | 29|  |
                            | |  |   |  |   |  |   |  |   |  |
                            0-ACE|   |  |   |  |   |  |   |  |
                              2-B3M  |  |   |  |   |  |   |  |
                                 5-BIL  |   |  |   |  |   |  |
                                     9-B3L  |  |   |  |   |  |
                                       12-BIL  |   |  |   |  |
                                           16-B3L  |  |   |  |
                                              19-BIL  |   |  |
                                                  23-B3L  |  |
   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 3F87)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3F87)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F87)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3F87)

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  3f87
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 Related Entries

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(-) Related Entries Specified in the PDB File

1gcl GCN4-PLI - TETRAMERIC, PARALLEL HELIX BUNDLE
2oxj GCN4-P1 WITH BETA RESIDUES AT B AND F HEPTAD POSITIONS
2oxk GCN4-PLI WITH BETA RESIDUES AT B AND F HEPTAD POSITIONS
2zta GCN4 LEUCINE ZIPPER - DIMERIC, PARALLEL COILED COIL