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 :  CRYSTAL STRUCTURE OF MONOBODY AS25/ABL1 SH2 DOMAIN COMPLEX, CRYSTAL B
 
Authors :  J. B. Wojcik, A. Koide, S. Koide
Date :  23 Aug 15  (Deposition) - 02 Mar 16  (Release) - 11 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.56
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Engineered Binding Protein, Antibody Mimic, Protein-Protein Complex, Sh2 Domain, Tyrosine-Protein Kinase, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Wojcik, A. J. Lamontanara, G. Grabe, A. Koide, L. Akin, B. Gerig, O. Hantschel, S. Koide
Allosteric Inhibition Of Bcr-Abl Kinase By High Affinity Monobody Inhibitors Directed To The Src Homology 2 (Sh2)-Kinase Interface.
J. Biol. Chem. V. 291 8836 2016
PubMed-ID: 26912659  |  Reference-DOI: 10.1074/JBC.M115.707901

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN KINASE ABL1
    Chains: A
    EC Number: 2.7.10.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHFT2
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ABL1, ABL, JTK7
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ABELSON MURINE LEUKEMIA VIRAL ONCOGENE HOMOLOG 1,ABELSON TYROSINE-PROTEIN KINASE 1,PROTO-ONCOGENE C-ABL,P150
 
Molecule 2 - AS25 MONOBODY
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHFT2
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2IMD2Ligand/IonIMIDAZOLE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:158 , LEU A:159 , SER A:161 , SER A:162 , ARG A:239 , HOH A:432 , GLY B:42 , GLY B:43 , TYR B:47 , TYR B:84binding site for residue GOL A 301
2AC2SOFTWARETYR A:191 , ILE A:229 , HOH A:489 , ALA B:14 , ALA B:15 , THR B:16 , SER B:19binding site for residue IMD A 302
3AC3SOFTWAREALA A:155 , TYR A:158 , HOH A:476 , PRO B:80 , LYS B:83 , TYR B:84binding site for residue IMD A 303
4AC4SOFTWAREHIS A:192 , HOH A:408 , PHE B:50 , VAL B:52 , LYS B:56 , ALA B:59 , THR B:60 , GOL B:102 , HOH B:239binding site for residue GOL B 101
5AC5SOFTWAREARG A:153 , HIS A:192 , PHE B:50 , SER B:62 , GOL B:101 , HOH B:233 , HOH B:234 , HOH B:247binding site for residue GOL B 102
6AC6SOFTWAREHOH A:403 , ASP B:32 , TYR B:33 , GLU B:51 , PRO B:53 , HOH B:205 , HOH B:216 , HOH B:237binding site for residues GOL B 103 and GOL B 104
7AC7SOFTWAREHOH A:403 , ASP B:32 , TYR B:33 , GLU B:51 , PRO B:53 , HOH B:205 , HOH B:216 , HOH B:237binding site for residues GOL B 103 and GOL B 104
8AC8SOFTWAREHOH A:403 , ASP B:32 , TYR B:33 , GLU B:51 , PRO B:53 , HOH B:205 , HOH B:216 , HOH B:237binding site for residues GOL B 103 and GOL B 104
9AC9SOFTWAREHOH A:403 , ASP B:32 , TYR B:33 , GLU B:51 , PRO B:53 , HOH B:205 , HOH B:216 , HOH B:237binding site for residues GOL B 103 and GOL B 104

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DC9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val B:6 -Pro B:7

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DC9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DC9)

(-) Exons   (0, 0)

(no "Exon" information available for 5DC9)

(-) 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:100
                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh..eeee.hhhhhhhhh......eeeeee.......eeeeeee..eeeeee.ee.....eeee..eee.hhhhhhhhhh...........ee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 5dc9 A 140 SLEKHSWYHGPVSRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYHYRINTASDGKLYVSSESRFNTLAELVHHHSTVADGLITTLHYPAPKR 239
                                   149       159       169       179       189       199       209       219       229       239


Chain B from PDB  Type:PROTEIN  Length:94
                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeeeee...eeeeee........eeeeeeee......eeeeeee....eeeee......eeeeeeeee........eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 5dc9 B   2 SVSDVPTKLEVVAATPTSLLISWDAPAVTVDYYVITYGETGGWSGYQEFEVPGSKSTATISGLSPGVDYTITVYAYGYPYVKYNKSPISINYRT  95
                                    11        21        31        41        51        61        71        81        91
   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 5DC9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DC9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DC9)

(-) Gene Ontology  (184, 188)

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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IMD  [ 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 ]
 
  Cis Peptide Bonds
    Val B:6 - Pro B:7   [ RasMol ]  
 

(-) 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
  5dc9
    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
  ABL1_HUMAN | P00519
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  FINC_HUMAN | P02751
    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)
  2.7.10.2
    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
  ABL1_HUMAN | P00519
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  FINC_HUMAN | P02751
    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
        ABL1_HUMAN | P00519: 1ab2 1abl 1awo 1bbz 1ju5 1opl 1zzp 2abl 2e2b 2f4j 2fo0 2g1t 2g2f 2g2h 2g2i 2gqg 2hiw 2hyy 2hz0 2hz4 2hzi 2o88 2v7a 3cs9 3eg0 3eg1 3eg2 3eg3 3egu 3k2m 3pyy 3qri 3qrj 3qrk 3t04 3ue4 3uyo 4j9b 4j9c 4j9d 4j9e 4j9f 4j9g 4j9h 4j9i 4jjb 4jjc 4jjd 4twp 4wa9 4xey 4yc8 4zog 5dc0 5dc4 5hu9 5mo4 5oaz
        FINC_HUMAN | P02751: 1e88 1e8b 1fbr 1fna 1fnf 1fnh 1j8k 1o9a 1oww 1q38 1qgb 1qo6 1ttf 1ttg 2cg6 2cg7 2ck2 2cku 2ec3 2fn2 2fnb 2gee 2h41 2h45 2ha1 2mnu 2n1k 2ocf 2rky 2rkz 2rl0 3cal 3ejh 3gxe 3m7p 3mql 3r8q 3t1w 3zrz 4gh7 4je4 4jeg 4lxo 4mmx 4mmy 4mmz 4pz5 5dc0 5dc4 5dft 5j6z 5j7c

(-) Related Entries Specified in the PDB File

5dc0 5DC0 CONTAINS A STRUCTURE OF ANOTHER MONOBODY/ABL SH2 DOMAIN COMPLEX
5dc4