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

(-) Description

Title :  PROTEIN TYROSINE PHOSPHATASE 1B DELTA HELIX 7, OPEN STATE
 
Authors :  M. S. Choy, W. Peti, R. Page
Date :  01 Jun 16  (Deposition) - 01 Mar 17  (Release) - 01 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Tyrosine Phosphatase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. S. Choy, Y. Li, L. E. Machado, M. B. Kunze, C. R. Connors, X. Wei, K. Lindorff-Larsen, R. Page, W. Peti
Conformational Rigidity And Protein Dynamics At Distinct Timescales Regulate Ptp1B Activity And Allostery.
Mol. Cell V. 65 644 2017
PubMed-ID: 28212750  |  Reference-DOI: 10.1016/J.MOLCEL.2017.01.014

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 1
    Chains: A
    EC Number: 3.1.3.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Gene: PTPN1, PTP1B
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTEIN-TYROSINE PHOSPHATASE 1B,PTP-1B

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric/Biological Unit (3, 13)
No.NameCountTypeFull Name
1CL9Ligand/IonCHLORIDE ION
2GOL3Ligand/IonGLYCEROL
3TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:54 , LYS A:128 , GLU A:129 , GLU A:130 , HOH A:454 , HOH A:511 , HOH A:527binding site for residue TRS A 301
02AC2SOFTWAREPRO A:89 , MET A:133 , PHE A:135 , HOH A:406 , HOH A:412binding site for residue GOL A 302
03AC3SOFTWARETYR A:46 , GLN A:262binding site for residue GOL A 303
04AC4SOFTWAREGLU A:76 , ARG A:238 , LYS A:248 , VAL A:249 , CL A:311binding site for residue GOL A 304
05AC5SOFTWAREPRO A:38 , LYS A:39binding site for residue CL A 305
06AC6SOFTWAREARG A:112 , VAL A:113 , HIS A:175binding site for residue CL A 306
07AC7SOFTWAREARG A:45binding site for residue CL A 307
08AC8SOFTWARETHR A:263 , HOH A:517binding site for residue CL A 308
09AC9SOFTWARELYS A:120 , CYS A:215 , SER A:216 , ARG A:221binding site for residue CL A 309
10AD1SOFTWAREARG A:79 , ARG A:199binding site for residue CL A 310
11AD2SOFTWAREARG A:238 , SER A:243 , ASP A:245 , GOL A:304binding site for residue CL A 311
12AD3SOFTWAREARG A:24 , ARG A:254binding site for residue CL A 312
13AD4SOFTWARESER A:151 , ASP A:181 , HOH A:575binding site for residue CL A 313

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KA0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5KA0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KA0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KA0)

(-) Exons   (0, 0)

(no "Exon" information available for 5KA0)

(-) 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:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhh...........eee.......eeeeeeeee....eeeeee......hhhhhhhhhhhhh..eeee....ee..ee.............eee....eeeeeeeeee...eeeeeeeeee.....eeeeeeeee...........hhhhhhhhhhhhhh.........eeee.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ka0 A   1 MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFI 281
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280
   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 5KA0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KA0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KA0)

(-) Gene Ontology  (51, 51)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TRS  [ 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 ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5ka0)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  5ka0
    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
  PTN1_HUMAN | P18031
    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)
  3.1.3.48
    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
  PTN1_HUMAN | P18031
    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
        PTN1_HUMAN | P18031: 1a5y 1aax 1bzc 1bzh 1bzj 1c83 1c84 1c85 1c86 1c87 1c88 1ecv 1een 1eeo 1g1f 1g1g 1g1h 1g7f 1g7g 1gfy 1i57 1jf7 1kak 1kav 1l8g 1lqf 1nl9 1nny 1no6 1nwe 1nwl 1nz7 1oem 1oeo 1oes 1oet 1oeu 1oev 1ony 1onz 1pa1 1ph0 1ptt 1ptu 1ptv 1pty 1pxh 1pyn 1q1m 1q6j 1q6m 1q6n 1q6p 1q6s 1q6t 1qxk 1sug 1t48 1t49 1t4j 1wax 1xbo 2azr 2b07 2b4s 2bgd 2bge 2cm2 2cm3 2cm7 2cm8 2cma 2cmb 2cmc 2cne 2cnf 2cng 2cnh 2cni 2f6f 2f6t 2f6v 2f6w 2f6y 2f6z 2f70 2f71 2fjm 2fjn 2h4g 2h4k 2hb1 2hnp 2hnq 2nt7 2nta 2qbp 2qbq 2qbr 2qbs 2veu 2vev 2vew 2vex 2vey 2zmm 2zn7 3a5j 3a5k 3cwe 3d9c 3eax 3eb1 3eu0 3i7z 3i80 3qkp 3qkq 3sme 3zmp 3zmq 3zv2 4bjo 4i8n 4qah 4qap 4qbe 4qbw 4y14 4zrt 5k9v 5k9w 5ka1 5ka2 5ka3 5ka4 5ka7 5ka8 5ka9 5kaa 5kab 5kac 5kad 5t19

(-) Related Entries Specified in the PDB File

5k9v 5k9w 5ka1 5ka2 5ka3 5ka4 5ka7 5ka8 5ka9 5kaa 5kab 5kac 5kad