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(-) Description

Title :  TRIMERIC HELIX BUNDLE FORMED BY AN ALPHA/BETA-PEPTIDE DERIVATIVE OF THE HIV GP41 CHR DOMAIN
 
Authors :  W. S. Horne, S. H. Gellman
Date :  03 Nov 08  (Deposition) - 15 Sep 09  (Release) - 20 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Alpha/Beta-Peptide, Helix Bundle, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. S. Horne, L. M. Johnson, T. J. Ketas, P. J. Klasse, M. Lu, J. P. Moore, S. H. Gellman
Structural And Biological Mimicry Of Protein Surface Recognition By Alpha/Beta-Peptide Foldamers
Proc. Natl. Acad. Sci. Usa V. 106 14751 2009
PubMed-ID: 19706443  |  Reference-DOI: 10.1073/PNAS.0902663106
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA/BETA-PEPTIDE ANALOGUE OF THE HIV GP41 CHR DOMAIN
    Chains: A, B, C
    Engineered: YES
    Other Details: THE PEPTIDE IS CHEMICALLY SYNTHESIZED. IT IS A SEQUENCE MUTANT TO A SEQUENCE THAT OCCURS NATURALLY IN HIV.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 43)

Asymmetric/Biological Unit (7, 43)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2B3E9Mod. Amino Acid(3S)-3-AMINOHEXANEDIOIC ACID
3B3T2Mod. Amino Acid3-AMINO-2,3,5-TRIDEOXY-D-THREO-PENTONIC ACID
4MPD8Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5NH21Mod. Amino AcidAMINO GROUP
6XCP12Mod. Amino Acid(1S,2S)-2-AMINOCYCLOPENTANECARBOXYLIC ACID
7XPC9Mod. Amino Acid(3S,4R)-4-AMINOPYRROLIDINE-3-CARBOXYLIC ACID

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREXCP A:19 , XPC A:22 , ALA A:23 , B3E B:12BINDING SITE FOR RESIDUE MPD A 40
2AC2SOFTWAREALA A:9 , HOH A:46 , ILE B:10 , MPD B:40BINDING SITE FOR RESIDUE MPD A 41
3AC3SOFTWAREXPC A:8 , ALA A:9 , HOH A:53 , XPC B:22 , ALA B:23 , HOH B:51BINDING SITE FOR RESIDUE MPD A 42
4AC4SOFTWAREARG A:16 , HOH A:55 , HOH A:63 , XCP B:15 , ARG B:16 , HOH B:53BINDING SITE FOR RESIDUE MPD A 43
5AC5SOFTWARETRP A:6 , ALA A:9 , MPD A:41 , TRP B:6 , ASP B:7 , ILE B:10BINDING SITE FOR RESIDUE MPD B 40
6AC6SOFTWAREXPC A:22 , B3E B:12 , XCP B:15BINDING SITE FOR RESIDUE MPD B 41
7AC7SOFTWAREALA A:24 , GLN A:27 , ALA B:24 , GLN B:25BINDING SITE FOR RESIDUE MPD B 42
8AC8SOFTWAREXCP C:5 , XPC C:8 , B3E C:12 , XCP C:19 , XPC C:22 , ALA C:23 , B3E C:26BINDING SITE FOR RESIDUE MPD C 40

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F4Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3F4Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3F4Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3F4Z)

(-) Exons   (0, 0)

(no "Exon" information available for 3F4Z)

(-) 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:39
                                                                      
               SCOP domains --------------------------------------- SCOP domains
               CATH domains --------------------------------------- CATH domains
               Pfam domains --------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------- PROSITE
                 Transcript --------------------------------------- Transcript
                  3f4z A  0 xxTWExWDxAIAeYAxRIExLIxAAQeQQeKNExALxEL 38
                            ||   |  |9  |  |  19  |   | 29   |  |  
                            ||   |  |   |  |   |  |   |  |   |  |  
                            0-ACE|  |   |  |   |  |   |  |   |  |  
                             1-B3T  |   |  |   |  |   |  |   |  |  
                                 5-XCP  |  |   |  |   |  |   |  |  
                                    8-XPC  |   |  |   |  |   |  |  
                                       12-B3E  |  |   |  |   |  |  
                                          15-XCP  |   |  |   |  |  
                                              19-XCP  |  |   |  |  
                                                 22-XPC  |   |  |  


Chain B from PDB  Type:PROTEIN  Length:34
                                                                 
               SCOP domains ---------------------------------- SCOP domains
               CATH domains ---------------------------------- CATH domains
               Pfam domains ---------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------- PROSITE
                 Transcript ---------------------------------- Transcript
                  3f4z B  5 xWDxAIAeYAxRIExLIxAAQeQQeKNExALxEL 38
                            |  |   |14|   |  |24 |  |   34 |  
                            |  |   |  |   |  |   |  |   |  |  
                            5-XCP  |  |   |  |   |  |   |  |  
                               8-XPC  |   |  |   |  |   |  |  
                                  12-B3E  |  |   |  |   |  |  
                                     15-XCP  |   |  |   |  |  
                                         19-XCP  |  |   |  |  
                                            22-XPC  |   |  |  
                                                26-B3E  |  |  
                                                   29-B3E  |  


Chain C from PDB  Type:PROTEIN  Length:40
                                                                       
               SCOP domains ---------------------------------------- SCOP domains
               CATH domains ---------------------------------------- CATH domains
               Pfam domains ---------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------- PROSITE
                 Transcript ---------------------------------------- Transcript
                  3f4z C  0 xxTWExWDxAIAeYAxRIExLIxAAQeQQeKNExALxELx 39
                            ||   |  |9  |  |  19  |   | 29   |  | 39
                            ||   |  |   |  |   |  |   |  |   |  |  |
                            0-ACE|  |   |  |   |  |   |  |   |  |  |
                             1-B3T  |   |  |   |  |   |  |   |  |  |
                                 5-XCP  |  |   |  |   |  |   |  |  |
                                    8-XPC  |   |  |   |  |   |  |  |
                                       12-B3E  |  |   |  |   |  |  |
                                          15-XCP  |   |  |   |  |  |
                                              19-XCP  |  |   |  |  |
                                                 22-XPC  |   |  |  |
   Legend:   → Mismatch (orange background)
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  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 3F4Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3F4Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F4Z)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3F4Z)

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 Related Entries

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(-) Related Entries Specified in the PDB File

3f4y 3f50