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 :  FOCAL ADHESION KINASE CATALYTIC DOMAIN
 
Authors :  J. Le Coq, A. Lin, D. Lietha
Date :  31 Oct 14  (Deposition) - 18 Feb 15  (Release) - 18 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase, Focal Adhesion Kinase, Kinase Inhibitor, Atp-Binding, Integrin Signaling (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Zhou, A. Bronowska, J. Le Coq, D. Lietha, F. Grater
Allosteric Regulation Of Focal Adhesion Kinase By Pip2 And Atp.
Biophys. J. V. 108 698 2015
PubMed-ID: 25650936  |  Reference-DOI: 10.1016/J.BPJ.2014.11.3454

(-) Compounds

Molecule 1 - FOCAL ADHESION KINASE
    Chains: A, B
    EC Number: 2.7.10.2
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HIGH FIVE
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: PACG2T
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: KINASE DOMAIN, RESIDUES 411-686
    Organism Common: CHICKEN
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031
    Synonym: FADK 1, FOCAL ADHESION KINASE-RELATED NONKINASE, FRNK, P41/P43FRNK, PROTEIN-TYROSINE KINASE 2, P125FAK, PP125FAK

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1DMS3Ligand/IonDIMETHYL SULFOXIDE
2KB81Ligand/Ion6-METHYL-4-(PIPERAZIN-1-YL)-2-(TRIFLUOROMETHYL)QUINOLINE
3SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1DMS2Ligand/IonDIMETHYL SULFOXIDE
2KB8-1Ligand/Ion6-METHYL-4-(PIPERAZIN-1-YL)-2-(TRIFLUOROMETHYL)QUINOLINE
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1DMS1Ligand/IonDIMETHYL SULFOXIDE
2KB81Ligand/Ion6-METHYL-4-(PIPERAZIN-1-YL)-2-(TRIFLUOROMETHYL)QUINOLINE
3SO43Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:482 , GLN A:529 , HOH A:2026BINDING SITE FOR RESIDUE DMS A1687
2AC2SOFTWAREGLY B:431 , GLN B:432 , PHE B:433 , GLY B:434BINDING SITE FOR RESIDUE DMS B1687
3AC3SOFTWAREILE A:428 , LEU A:553 , HOH A:2018BINDING SITE FOR RESIDUE DMS A1688
4AC4SOFTWARESER A:601 , ARG A:668 , HOH A:2062BINDING SITE FOR RESIDUE SO4 A1689
5AC5SOFTWARELYS A:621 , GLN A:624 , ASP B:519 , LEU B:520 , ASN B:646 , HOH B:2015BINDING SITE FOR RESIDUE SO4 B1688
6AC6SOFTWAREHIS B:480 , LYS B:673 , HOH B:2017BINDING SITE FOR RESIDUE SO4 B1689
7AC7SOFTWAREARG B:508 , GLN B:512BINDING SITE FOR RESIDUE SO4 B1690
8AC8SOFTWAREILE B:428 , VAL B:436 , ALA B:452 , LYS B:454 , MET B:499 , GLU B:500 , GLU B:506 , LEU B:553 , GLY B:563 , HOH B:2010 , HOH B:2032BINDING SITE FOR RESIDUE KB8 B1691

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4D4V)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:493 -Pro A:494
2Asn B:493 -Pro B:494

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4D4V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4D4V)

(-) Exons   (0, 0)

(no "Exon" information available for 4D4V)

(-) 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:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhh.eeeeeeee......eeeeee.......eeeeeee.....hhhhhhhhhhhhhhhhh........eeeee.....eeeee.....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eeeee..eeee......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d4v A 415 YEIQRERIELGRCIGEGQFGDVHQGIYMSPENPAMAVAIKTCKNCTSDSVREKFLQEALTMRQFDHPHIVKLIGVITENPVWIIMELCTLGELRSFLQVRKFSLDLASLILYAYQLSTALAYLESKRFVHRDIAARNVLVSATDCVKLGDFGKLPIKWMAPESINFRRFTSASDVWMFGVCMWEILMHGVKPFQGVKNNDVIGRIENGERLPMPPNCPPTLYSLMTKCWAYDPSRRPRFTELKAQLSTILEEEKLQ 686
                                   424       434       444       454       464       474       484       494       504       514       524       534       544       554       564 ||    590       600       610       620       630       640       650       660       670       680      
                                                                                                                                                                                 566|                                                                                                       
                                                                                                                                                                                  583                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:255
                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhh.eeeeeeee......eeeeee.......eeeeeee.....hhhhhhhhhhhhhhhhh........eeeee.....eeeee....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhh.eeeee..eeee.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d4v B 415 YEIQRERIELGRCIGEGQFGDVHQGIYMSPENPAMAVAIKTCKNCTSDSVREKFLQEALTMRQFDHPHIVKLIGVITENPVWIIMELCTLGELRSFLQVRKFSLDLASLILYAYQLSTALAYLESKRFVHRDIAARNVLVSATDCVKLGDFGLPIKWMAPESINFRRFTSASDVWMFGVCMWEILMHGVKPFQGVKNNDVIGRIENGERLPMPPNCPPTLYSLMTKCWAYDPSRRPRFTELKAQLSTILEEEKLQ 686
                                   424       434       444       454       464       474       484       494       504       514       524       534       544       554       564 ||    591       601       611       621       631       641       651       661       671       681     
                                                                                                                                                                                 566|                                                                                                      
                                                                                                                                                                                  584
   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 4D4V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D4V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D4V)

(-) Gene Ontology  (50, 50)

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
    DMS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    KB8  [ 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 ]
 
  Cis Peptide Bonds
    Asn A:493 - Pro A:494   [ RasMol ]  
    Asn B:493 - Pro B:494   [ RasMol ]  
 
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
  4d4v
    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
  FAK1_CHICK | Q00944
    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
  FAK1_CHICK | Q00944
    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
        FAK1_CHICK | Q00944: 1ktm 1pv3 1qvx 2aeh 2al6 2j0j 2j0k 2j0l 2j0m 2jkk 2jkm 2jko 2jkq 2l6f 2l6g 2l6h 3zdt 4brx 4c7t 4cye 4d4r 4d4s 4d4y 4d55 4d58 4d5h 4d5k

(-) Related Entries Specified in the PDB File

4d4r FOCAL ADHESION KINASE CATALYTIC DOMAIN
4d4s FOCAL ADHESION KINASE CATALYTIC DOMAIN
4d4y FOCAL ADHESION KINASE CATALYTIC DOMAIN
4d55 FOCAL ADHESION KINASE CATALYTIC DOMAIN
4d58 FOCAL ADHESION KINASE CATALYTIC DOMAIN IN COMPLEX WITH BIS-ANILINO PYRIMIDINE INHIBITOR
4d5h FOCAL ADHESION KINASE CATALYTIC DOMAIN
4d5k FOCAL ADHESION KINASE CATALYTIC DOMAIN