Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
(-)Biological Unit 5
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)
Image Biological Unit 5
Biological Unit 5  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF A DE NOVO DESIGNED TRIMERIC COILED-COIL PEPTIDE
 
Authors :  P. Burkhard, M. Meier, A. Lustig
Date :  18 Dec 00  (Deposition) - 14 Mar 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Biol. Unit 3:  G,H,I  (1x)
Biol. Unit 4:  J,K,L  (1x)
Biol. Unit 5:  A (1x),B (1x),C (1x),D (1x),E (1x),F (1x),G (1x),H (1x),I (1x),J (1x),K (1x),L (1x)
Keywords :  Coiled Coil, De Novo Design, Alpha-Helix, Trimer, De Novo Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Burkhard, M. Meier, A. Lustig
Design Of A Minimal Protein Oligomerization Domain By A Structural Approach.
Protein Sci. V. 9 2294 2000
PubMed-ID: 11206050
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU- ALA-ARG-ILE-LYS-NH2
    Chains: A, B, C, D, E, F, G, H, I, J, K, L
    Engineered: YES
    Other Details: NEOSYSTEM
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): ABC         
Biological Unit 2 (1x):    DEF      
Biological Unit 3 (1x):       GHI   
Biological Unit 4 (1x):          JKL
Biological Unit 5 (1x): A (1x)B (1x)C (1x)D (1x)E (1x)F (1x)G (1x)H (1x)I (1x)J (1x)K (1x)L (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 25)

Asymmetric Unit (3, 25)
No.NameCountTypeFull Name
1PB9Ligand/IonLEAD (II) ION
2SIN12Ligand/IonSUCCINIC ACID
3SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1PB-1Ligand/IonLEAD (II) ION
2SIN3Ligand/IonSUCCINIC ACID
3SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1PB-1Ligand/IonLEAD (II) ION
2SIN3Ligand/IonSUCCINIC ACID
3SO41Ligand/IonSULFATE ION
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1PB-1Ligand/IonLEAD (II) ION
2SIN3Ligand/IonSUCCINIC ACID
3SO41Ligand/IonSULFATE ION
Biological Unit 4 (1, 3)
No.NameCountTypeFull Name
1PB-1Ligand/IonLEAD (II) ION
2SIN3Ligand/IonSUCCINIC ACID
3SO4-1Ligand/IonSULFATE ION
Biological Unit 5 (2, 7)
No.NameCountTypeFull Name
1PB-1Ligand/IonLEAD (II) ION
2SIN6Ligand/IonSUCCINIC ACID
3SO41Ligand/IonSULFATE ION

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG B:14 , ARG J:9 , ARG K:7BINDING SITE FOR RESIDUE SO4 B 1001
02AC2SOFTWAREARG D:7 , ARG F:9 , ARG G:14 , HOH G:2008 , LYS I:16BINDING SITE FOR RESIDUE SO4 F 1002
03AC3SOFTWAREARG H:9 , ARG I:7 , LYS K:16 , ARG L:14BINDING SITE FOR RESIDUE SO4 I 1003
04AC4SOFTWAREARG A:7 , ARG C:9 , ARG E:14BINDING SITE FOR RESIDUE SO4 C 1004
05AC5SOFTWAREHOH G:2008 , SIN K:1 , LEU K:4BINDING SITE FOR RESIDUE PB G 2001
06AC6SOFTWARESIN D:1 , LEU D:4BINDING SITE FOR RESIDUE PB D 2002
07AC7SOFTWAREGLU A:10 , HOH C:1007 , HOH C:1011BINDING SITE FOR RESIDUE PB A 2003
08AC8SOFTWAREASP F:2BINDING SITE FOR RESIDUE PB F 2004
09AC9SOFTWARESIN A:1 , HOH A:2008 , LYS K:16BINDING SITE FOR RESIDUE PB K 2005
10BC1SOFTWAREHOH H:2013 , HOH H:2020 , GLU I:10BINDING SITE FOR RESIDUE PB I 2006
11BC2SOFTWAREGLU E:10 , HOH E:2019 , ASP H:2BINDING SITE FOR RESIDUE PB E 2007
12BC3SOFTWAREGLU F:10 , SIN H:1 , GLU H:3BINDING SITE FOR RESIDUE PB H 2008
13BC4SOFTWAREGLU A:5 , GLU L:3BINDING SITE FOR RESIDUE PB L 2009
14BC5SOFTWAREASP A:2 , GLU A:3 , LEU A:4 , GLU A:5 , HOH A:2007 , HOH A:2008 , GLU K:12 , PB K:2005 , ARG L:7BINDING SITE FOR RESIDUE SIN A 1
15BC6SOFTWAREASP B:2 , GLU B:3 , LEU B:4 , GLU B:5 , HOH B:1011 , ASP L:2 , GLU L:3BINDING SITE FOR RESIDUE SIN B 1
16BC7SOFTWAREASP C:2 , GLU C:3 , LEU C:4 , GLU C:5 , HOH C:1010 , HOH C:1014 , HOH C:1016 , ARG L:6 , GLU L:10BINDING SITE FOR RESIDUE SIN C 1
17BC8SOFTWAREGLU A:12 , HOH A:2009 , HOH A:2010 , ARG B:7 , ASP D:2 , GLU D:3 , LEU D:4 , GLU D:5 , PB D:2002BINDING SITE FOR RESIDUE SIN D 1
18BC9SOFTWAREGLU B:3 , ASP E:2 , GLU E:3 , LEU E:4 , GLU E:5 , HOH E:2016BINDING SITE FOR RESIDUE SIN E 1
19CC1SOFTWAREARG B:6 , HOH B:1003 , LEU D:4 , HOH E:2020 , ASP F:2 , GLU F:3 , LEU F:4 , GLU F:5 , HOH F:2009 , HOH F:2010BINDING SITE FOR RESIDUE SIN F 1
20CC2SOFTWAREASP E:2 , GLU E:3 , ARG E:6 , ASP G:2 , GLU G:3 , LEU G:4 , GLU G:5 , HOH G:2004 , HOH G:2011BINDING SITE FOR RESIDUE SIN G 1
21CC3SOFTWAREASP H:2 , GLU H:3 , LEU H:4 , GLU H:5 , PB H:2008BINDING SITE FOR RESIDUE SIN H 1
22CC4SOFTWARELYS D:16 , ARG E:6 , GLU E:10 , HOH E:2015 , ASP I:2 , GLU I:3 , LEU I:4 , GLU I:5BINDING SITE FOR RESIDUE SIN I 1
23CC5SOFTWAREARG G:6 , HOH G:2006 , HOH G:2010 , HOH G:2012 , ASP J:2 , GLU J:3 , LEU J:4 , GLU J:5 , LEU K:4BINDING SITE FOR RESIDUE SIN J 1
24CC6SOFTWAREARG G:7 , PB G:2001 , GLU I:12 , HOH I:2009 , HOH I:2012 , ASP K:2 , GLU K:3 , LEU K:4 , GLU K:5BINDING SITE FOR RESIDUE SIN K 1
25CC7SOFTWAREGLU G:3 , HOH G:2009 , ASP L:2 , GLU L:3 , LEU L:4 , GLU L:5BINDING SITE FOR RESIDUE SIN L 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1HQJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1HQJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1HQJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1HQJ)

(-) Exons   (0, 0)

(no "Exon" information available for 1HQJ)

(-) 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:15
                                              
               SCOP domains d1hqja_ A:      SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                  1hqj A  2 DELERRIRELEARIK 16
                                    11     


Chain B from PDB  Type:PROTEIN  Length:15
                                              
               SCOP domains d1hqjb_ B:      SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                  1hqj B  2 DELERRIRELEARIK 16
                                    11     


Chain C from PDB  Type:PROTEIN  Length:15
                                              
               SCOP domains d1hqjc_ C:      SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                  1hqj C  2 DELERRIRELEARIK 16
                                    11     


Chain D from PDB  Type:PROTEIN  Length:15
                                              
               SCOP domains d1hqjd_ D:      SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                  1hqj D  2 DELERRIRELEARIK 16
                                    11     


Chain E from PDB  Type:PROTEIN  Length:15
                                              
               SCOP domains d1hqje_ E:      SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                  1hqj E  2 DELERRIRELEARIK 16
                                    11     


Chain F from PDB  Type:PROTEIN  Length:15
                                              
               SCOP domains d1hqjf_ F:      SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                  1hqj F  2 DELERRIRELEARIK 16
                                    11     


Chain G from PDB  Type:PROTEIN  Length:15
                                              
               SCOP domains d1hqjg_ G:      SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                  1hqj G  2 DELERRIRELEARIK 16
                                    11     


Chain H from PDB  Type:PROTEIN  Length:15
                                              
               SCOP domains d1hqjh_ H:      SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                  1hqj H  2 DELERRIRELEARIK 16
                                    11     


Chain I from PDB  Type:PROTEIN  Length:15
                                              
               SCOP domains d1hqji_ I:      SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                  1hqj I  2 DELERRIRELEARIK 16
                                    11     


Chain J from PDB  Type:PROTEIN  Length:15
                                              
               SCOP domains d1hqjj_ J:      SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                  1hqj J  2 DELERRIRELEARIK 16
                                    11     


Chain K from PDB  Type:PROTEIN  Length:15
                                              
               SCOP domains d1hqjk_ K:      SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                  1hqj K  2 DELERRIRELEARIK 16
                                    11     


Chain L from PDB  Type:PROTEIN  Length:15
                                              
               SCOP domains d1hqjl_ L:      SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                  1hqj L  2 DELERRIRELEARIK 16
                                    11
   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  (1, 12)

Asymmetric Unit
(-)
Class: Designed proteins (167)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1HQJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HQJ)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1HQJ)

 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
    PB  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SIN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
    CC4  [ RasMol ]  +environment [ RasMol ]
    CC5  [ RasMol ]  +environment [ RasMol ]
    CC6  [ RasMol ]  +environment [ RasMol ]
    CC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1hqj)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]
    Biological Unit 5  [ 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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 PNG format | Biol. Unit 5 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
  1hqj
    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 1HQJ)

(-) Related Entries Specified in the PDB File

1d7m THE COILED-COIL TRIGGER SITE OF THE ROD DOMAIN OF CORTEXILLIN I
1gcm CONTROL PROTEIN GCN4, AMINO ACID BIOSYNTHESIS REGULATORY PROTEIN; ENGINEERED: YES; MUTATION: L5I, V9I, L12I, N16I, L19I, V23I, L26I, V30I (I AT HEPTAD A POSITIONS, I AT HEPTAD D POSITIONS)