Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF AN ALKYLATED CYS MUTANT OF CC-HEX
 
Authors :  A. J. Burton, C. Agnew, R. L. Brady, D. N. Woolfson
Date :  23 May 13  (Deposition) - 21 Aug 13  (Release) - 11 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,B,C,D,E,F  (1x)
Biol. Unit 2:  G,H,I,J,K,L  (1x)
Keywords :  De Novo Coiled-Coil Assembly, De Novo Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. J. Burton, F. Thomas, C. Agnew, K. L. Hudson, S. E. Halford, R. L. Brady, D. N. Woolfson
Accessibility, Reactivity, And Selectivity Of Side Chains Within A Channel Of De Novo Peptide Assembly.
J. Am. Chem. Soc. V. 135 12524 2013
PubMed-ID: 23924058  |  Reference-DOI: 10.1021/JA4053027

(-) Compounds

Molecule 1 - 6-HELIX COILED COIL CC-HEX-L24C PEPTIDE WITH AN ALKYLATED CYS MUTATION
    Chains: A, B, C, D, E, F, G, H, I, J, K, L
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): ABCDEF      
Biological Unit 2 (1x):       GHIJKL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 36)

Asymmetric Unit (3, 36)
No.NameCountTypeFull Name
14BF12Mod. Amino Acid4-BROMO-L-PHENYLALANINE
2ACE12Mod. Amino AcidACETYL GROUP
3YCM12Mod. Amino AcidS-(2-AMINO-2-OXOETHYL)-L-CYSTEINE
Biological Unit 1 (3, 18)
No.NameCountTypeFull Name
14BF6Mod. Amino Acid4-BROMO-L-PHENYLALANINE
2ACE6Mod. Amino AcidACETYL GROUP
3YCM6Mod. Amino AcidS-(2-AMINO-2-OXOETHYL)-L-CYSTEINE
Biological Unit 2 (3, 18)
No.NameCountTypeFull Name
14BF6Mod. Amino Acid4-BROMO-L-PHENYLALANINE
2ACE6Mod. Amino AcidACETYL GROUP
3YCM6Mod. Amino AcidS-(2-AMINO-2-OXOETHYL)-L-CYSTEINE

(-) Sites  (0, 0)

(no "Site" information available for 4KVV)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KVV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4KVV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KVV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KVV)

(-) Exons   (0, 0)

(no "Exon" information available for 4KVV)

(-) 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
                                                             
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                  4kvv A  0 xGELKAIAQELKAIAKELKAIAyEcKAIAQ 29
                            |        9        19  | |   29
                            |                    22-4BF   
                            0-ACE                  24-YCM 


Chain B from PDB  Type:PROTEIN  Length:29
                                                            
               SCOP domains ----------------------------- SCOP domains
               CATH domains ----------------------------- CATH domains
               Pfam domains ----------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------- SAPs(SNPs)
                    PROSITE ----------------------------- PROSITE
                 Transcript ----------------------------- Transcript
                  4kvv B  0 xGELKAIAQELKAIAKELKAIAyEcKAIA 28
                            |        9        19  | |    
                            0-ACE                22-4BF  
                                                   24-YCM


Chain C from PDB  Type:PROTEIN  Length:28
                                                           
               SCOP domains ---------------------------- SCOP domains
               CATH domains ---------------------------- CATH domains
               Pfam domains ---------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------- PROSITE
                 Transcript ---------------------------- Transcript
                  4kvv C  0 xGELKAIAQELKAIAKELKAIAyEcKAI 27
                            |        9        19  | |   
                            |                    22-4BF 
                            0-ACE                  24-YCM


Chain D from PDB  Type:PROTEIN  Length:30
                                                             
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                  4kvv D  0 xGELKAIAQELKAIAKELKAIAyEcKAIAQ 29
                            |        9        19  | |   29
                            |                    22-4BF   
                            0-ACE                  24-YCM 


Chain E from PDB  Type:PROTEIN  Length:29
                                                            
               SCOP domains ----------------------------- SCOP domains
               CATH domains ----------------------------- CATH domains
               Pfam domains ----------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------- SAPs(SNPs)
                    PROSITE ----------------------------- PROSITE
                 Transcript ----------------------------- Transcript
                  4kvv E  0 xGELKAIAQELKAIAKELKAIAyEcKAIA 28
                            |        9        19  | |    
                            0-ACE                22-4BF  
                                                   24-YCM


Chain F from PDB  Type:PROTEIN  Length:30
                                                             
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                  4kvv F  0 xGELKAIAQELKAIAKELKAIAyEcKAIAQ 29
                            |        9        19  | |   29
                            |                    22-4BF   
                            0-ACE                  24-YCM 


Chain G from PDB  Type:PROTEIN  Length:29
                                                            
               SCOP domains ----------------------------- SCOP domains
               CATH domains ----------------------------- CATH domains
               Pfam domains ----------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------- SAPs(SNPs)
                    PROSITE ----------------------------- PROSITE
                 Transcript ----------------------------- Transcript
                  4kvv G  0 xGELKAIAQELKAIAKELKAIAyEcKAIA 28
                            |        9        19  | |    
                            0-ACE                22-4BF  
                                                   24-YCM


Chain H from PDB  Type:PROTEIN  Length:31
                                                              
               SCOP domains ------------------------------- SCOP domains
               CATH domains ------------------------------- CATH domains
               Pfam domains ------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------- PROSITE
                 Transcript ------------------------------- Transcript
                  4kvv H  0 xGELKAIAQELKAIAKELKAIAyEcKAIAQG 30
                            |        9        19  | |   29 
                            |                    22-4BF    
                            0-ACE                  24-YCM  


Chain I from PDB  Type:PROTEIN  Length:30
                                                             
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                  4kvv I  0 xGELKAIAQELKAIAKELKAIAyEcKAIAQ 29
                            |        9        19  | |   29
                            0-ACE                22-4BF   
                                                   24-YCM 


Chain J from PDB  Type:PROTEIN  Length:29
                                                            
               SCOP domains ----------------------------- SCOP domains
               CATH domains ----------------------------- CATH domains
               Pfam domains ----------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------- SAPs(SNPs)
                    PROSITE ----------------------------- PROSITE
                 Transcript ----------------------------- Transcript
                  4kvv J  0 xGELKAIAQELKAIAKELKAIAyEcKAIA 28
                            |        9        19  | |    
                            0-ACE                22-4BF  
                                                   24-YCM


Chain K from PDB  Type:PROTEIN  Length:30
                                                             
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                  4kvv K  0 xGELKAIAQELKAIAKELKAIAyEcKAIAQ 29
                            |        9        19  | |   29
                            |                    22-4BF   
                            0-ACE                  24-YCM 


Chain L from PDB  Type:PROTEIN  Length:31
                                                              
               SCOP domains ------------------------------- SCOP domains
               CATH domains ------------------------------- CATH domains
               Pfam domains ------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------- PROSITE
                 Transcript ------------------------------- Transcript
                  4kvv L  0 xGELKAIAQELKAIAKELKAIAyEcKAIAQG 30
                            |        9        19  | |   29 
                            0-ACE                22-4BF    
                                                   24-YCM
   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 4KVV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KVV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KVV)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4KVV)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    4BF  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ACE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    YCM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 4kvv)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4kvv)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4kvv
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4KVV)

(-) Related Entries Specified in the PDB File

3r3k CRYSTAL STRUCTURE OF A PARALLEL 6-HELIX COILED COIL
4kvt CRYSTAL STRUCTURE OF A 6-HELIX COILED COIL CC-HEX-L24C
4kvu CRYSTAL STRUCTURE OF A 6-HELIX COILED COIL CC-HEX-L17C- W224BF