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
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)

(-) Description

Title :  TAX-INTERACTING PROTEIN-1 (TIP-1) PDZ DOMAIN BOUND TO Y-ICAL36 (YPTSII) PEPTIDE
 
Authors :  J. F. Amacher, D. R. Madden
Date :  18 Nov 13  (Deposition) - 21 Jan 15  (Release) - 21 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Tax-Interacting Protein-1, Tip-1, Pdz, Pdz-Peptide, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. R. Cushing, J. F. Amacher, L. Vouilleme, S. Culatti, B. Deng, S. A. Gerber, P. Boisguerin, D. R. Madden
A Cal Inhibitor With Single-Pdz Specificity Rescues Deltaf508-Cftr
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TAX1-BINDING PROTEIN 3
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET16B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TAX1BP3, TIP1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GLUTAMINASE-INTERACTING PROTEIN 3, TAX INTERACTION PROTEIN 1, TIP-1, TAX-INTERACTING PROTEIN 1
 
Molecule 2 - TIP-1 PDZ DOMAIN
    Chains: C, D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:114 , LEU A:115 , LYS A:117BINDING SITE FOR RESIDUE GOL A 201
2AC2SOFTWAREASN B:27 , LEU B:28 , THR B:99 , ARG B:101 , ALA B:118 , GLN B:121 , HOH B:303BINDING SITE FOR RESIDUE GOL B 201
3AC3SOFTWAREVAL A:14 , ARG A:16 , ILE A:29 , LEU A:30 , GLY A:31 , PHE A:32 , SER A:33 , ILE A:34 , GLY A:35 , GLY A:36 , GLN A:40 , GLN A:44 , ASN A:45 , THR A:59 , ARG A:60 , HIS A:91 , ARG A:95 , LEU A:98 , THR A:99 , GLN A:120 , GLN A:121 , HOH A:319 , HOH A:356 , HOH A:385 , HOH C:101 , HOH C:102 , HOH C:104 , HOH C:105 , HOH C:106BINDING SITE FOR CHAIN C OF TIP-1 PDZ DOMAIN
4AC4SOFTWAREVAL B:14 , ARG B:16 , ILE B:29 , LEU B:30 , GLY B:31 , PHE B:32 , SER B:33 , ILE B:34 , GLY B:35 , GLY B:36 , GLN B:40 , GLN B:44 , ASN B:45 , THR B:59 , ARG B:60 , HIS B:91 , ARG B:95 , LEU B:98 , THR B:99 , GLN B:120 , GLN B:121 , HOH B:369 , HOH D:101 , HOH D:102 , HOH D:103 , HOH D:104BINDING SITE FOR CHAIN D OF TIP-1 PDZ DOMAIN

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NNM)

(-) 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:111
                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.eee..eee..eeeee....hhhhh..........eeeeee...hhhhhhh.....eeeee..ee....hhhhhhhhhh.....eeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 4nnm A  11 TAVVQRVEIHKLRQGENLILGFSIGGGIDQDPSQNPFSEDKTDKGIYVTRVSEGGPAEIAGLQIGDKIMQVNGWDMTMVTHDQARKRLTKRSEEVVRLLVTRQSLQKAVQQ 121
                                    20        30        40        50        60        70        80        90       100       110       120 


Chain B from PDB  Type:PROTEIN  Length:112
                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee.eee..eee..eeeee....hhhhh..........eeeeee...hhhhhhh.....eeeee..ee....hhhhhhhhhh.....eeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 4nnm B  10 VTAVVQRVEIHKLRQGENLILGFSIGGGIDQDPSQNPFSEDKTDKGIYVTRVSEGGPAEIAGLQIGDKIMQVNGWDMTMVTHDQARKRLTKRSEEVVRLLVTRQSLQKAVQQ 121
                                    19        29        39        49        59        69        79        89        99       109       119  


Chain C from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ..eeee Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 4nnm C   5 YPTSII  10


Chain D from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ..eeee Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 4nnm D   5 YPTSII  10
   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 4NNM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4nnm)
 
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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites 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
  4nnm
    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
  TX1B3_HUMAN | O14907
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  TX1B3_HUMAN | O14907
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TX1B3_HUMAN | O14907: 2kg2 2l4s 2l4t 2vz5 3gj9 3sfj 4e3b 4nnl

(-) Related Entries Specified in the PDB File

4nnl