Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
(-)Biological Unit 5
(-)Biological Unit 6
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
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)
Image Biological Unit 6
Biological Unit 6  (Jmol Viewer)

(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF A CHEMICALLY SYNTHESIZED [D-GLN35]UBIQUITIN
 
Authors :  D. Bang, G. I. Makhatadze, V. Tereshko, A. A. Kossiakoff, S. B. Kent
Date :  13 Jan 05  (Deposition) - 14 Jun 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  A,B,C  (1x)
Biol. Unit 5:  A (1x),B (1x),C (1x)
Biol. Unit 6:  A (1x),B (1x)
Keywords :  Ubiquitin, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Bang, G. I. Makhatadze, V. Tereshko, A. A. Kossiakoff, S. B. Kent
X-Ray Crystal Structure Of A Chemically Synthesized [D-Gln35]Ubiquitin
Angew. Chem. Int. Ed. Engl. V. 44 3852 2005
PubMed-ID: 15834850  |  Reference-DOI: 10.1002/ANIE.200463040

(-) Compounds

Molecule 1 - UBIQUITIN
    Chains: A, B, C
    Engineered: YES
    Fragment: RESIDUES 1-76
    Mutation: YES
    Other Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PROTEIN CAN BE NATURALLY FOUND IN HOMO SAPIENS (HUMAN)
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C
Biological Unit 4 (1x): ABC
Biological Unit 5 (1x): A (1x)B (1x)C (1x)
Biological Unit 6 (1x): A (1x)B (1x) 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 23)

Asymmetric Unit (3, 23)
No.NameCountTypeFull Name
1CD17Ligand/IonCADMIUM ION
2CL3Ligand/IonCHLORIDE ION
3DGN3Mod. Amino AcidD-GLUTAMINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2CL-1Ligand/IonCHLORIDE ION
3DGN1Mod. Amino AcidD-GLUTAMINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2CL-1Ligand/IonCHLORIDE ION
3DGN1Mod. Amino AcidD-GLUTAMINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2CL-1Ligand/IonCHLORIDE ION
3DGN1Mod. Amino AcidD-GLUTAMINE
Biological Unit 4 (1, 3)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2CL-1Ligand/IonCHLORIDE ION
3DGN3Mod. Amino AcidD-GLUTAMINE
Biological Unit 5 (1, 1)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2CL-1Ligand/IonCHLORIDE ION
3DGN1Mod. Amino AcidD-GLUTAMINE
Biological Unit 6 (1, 1)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2CL-1Ligand/IonCHLORIDE ION
3DGN1Mod. Amino AcidD-GLUTAMINE

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECL A:91 , CL A:92 , HOH A:95 , CL B:93 , HOH C:96 , HOH C:1341BINDING SITE FOR RESIDUE CD A 90
02AC2SOFTWARESER A:20 , ASP A:21 , CD A:90 , ASN C:25 , HOH C:1341BINDING SITE FOR RESIDUE CL A 91
03AC3SOFTWAREASN A:25 , CD A:90 , SER B:20 , ASP B:21 , HOH B:203BINDING SITE FOR RESIDUE CL A 92
04AC4SOFTWARECD A:90 , ASN B:25 , SER C:20 , ASP C:21BINDING SITE FOR RESIDUE CL B 93
05AC5SOFTWAREASP A:21 , HOH A:102 , HOH A:103 , GLU B:18BINDING SITE FOR RESIDUE CD A 101
06AC6SOFTWAREGLU A:24 , ASP A:52 , HOH A:105 , HOH A:106 , HOH A:107BINDING SITE FOR RESIDUE CD A 104
07AC7SOFTWAREHIS A:68 , HOH A:109 , HOH A:110 , HOH A:111 , HOH A:112 , HOH A:113BINDING SITE FOR RESIDUE CD A 108
08AC8SOFTWAREASP A:58 , HOH A:115 , HOH A:116 , HOH A:117 , HOH C:118BINDING SITE FOR RESIDUE CD A 114
09AC9SOFTWAREHOH A:120 , HOH A:121 , HOH A:122 , HOH A:123 , HOH A:124 , HOH B:1234BINDING SITE FOR RESIDUE CD A 119
10BC1SOFTWAREASP B:21 , HOH B:202 , HOH B:203 , GLU C:18BINDING SITE FOR RESIDUE CD B 201
11BC2SOFTWAREGLU B:24 , ASP B:52 , HOH B:205 , HOH B:206 , HOH B:207BINDING SITE FOR RESIDUE CD B 204
12BC3SOFTWAREHIS B:68 , HOH B:209 , HOH B:210 , HOH B:211 , HOH B:212 , HOH B:213BINDING SITE FOR RESIDUE CD B 208
13BC4SOFTWAREASP B:58 , HOH B:215 , HOH B:216 , HOH C:217 , HOH C:218BINDING SITE FOR RESIDUE CD B 214
14BC5SOFTWAREGLU B:64 , HOH B:227 , HOH B:228 , HOH C:1334BINDING SITE FOR RESIDUE CD B 225
15BC6SOFTWAREASP B:39 , HOH B:230 , HOH B:231BINDING SITE FOR RESIDUE CD B 229
16BC7SOFTWAREGLU A:18 , HOH A:303 , ASP C:21 , HOH C:302BINDING SITE FOR RESIDUE CD A 301
17BC8SOFTWAREGLU C:24 , ASP C:52 , HOH C:305 , HOH C:306 , HOH C:307BINDING SITE FOR RESIDUE CD C 304
18BC9SOFTWAREASP A:39 , HIS C:68 , HOH C:309 , HOH C:310 , HOH C:311BINDING SITE FOR RESIDUE CD C 308
19CC1SOFTWAREASP C:58 , HOH C:315 , HOH C:316 , HOH C:317 , HOH C:318BINDING SITE FOR RESIDUE CD C 314
20CC2SOFTWAREGLU C:64 , HOH C:1346BINDING SITE FOR RESIDUE CD C 325

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YJ1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YJ1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YJ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YJ1)

(-) Exons   (0, 0)

(no "Exon" information available for 1YJ1)

(-) 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:71
                                                                                                      
               SCOP domains d1yj1a1 A:1-71 Ubiquitin                                                SCOP domains
               CATH domains 1yj1A00 A:1-71                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhhhh.eee..ee......hhhhh.....eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  1yj1 A  1 LQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKExIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL 71
                                    10        20        30    |   40        50        60        70 
                                                             35-DGN                                


Chain B from PDB  Type:PROTEIN  Length:72
                                                                                                       
               SCOP domains d1yj1b1 B:1-71 Ubiquitin                                               - SCOP domains
               CATH domains 1yj1B00 B:1-72                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhhhheeee..ee......hhhhh.....eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                  1yj1 B  1 LQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKExIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72
                                    10        20        30    |   40        50        60        70  
                                                             35-DGN                                 


Chain C from PDB  Type:PROTEIN  Length:74
                                                                                                         
               SCOP domains d1yj1c1 C:1-71 Ubiquitin                                               --- SCOP domains
               CATH domains 1yj1C00 C:1-74                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                  1yj1 C  1 LQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKExIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 74
                                    10        20        30    |   40        50        60        70    
                                                             35-DGN
   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, 3)

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

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1YJ1)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1YJ1)

 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
    CD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DGN  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1yj1)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]
    Biological Unit 5  [ Jena3D ]
    Biological Unit 6  [ 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 | Biol. Unit 6 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
  1yj1
    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 1YJ1)

(-) Related Entries Specified in the PDB File

1yiw WILD TYPE UBIQUITIN