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 :  IN CELLULO CRYSTAL STRUCTURE OF PAK4 IN COMPLEX WITH INKA
 
Authors :  Y. Baskaran, K. C. Ang, P. V. Anekal, W. L. Chan, J. M. Grimes, E. Manser, R. C. Robinson
Date :  17 Dec 14  (Deposition) - 02 Dec 15  (Release) - 09 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.94
Chains :  Asym./Biol. Unit :  A
Keywords :  Pak4, Inka, Crystallization, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Baskaran, K. C. Ang, P. V. Anekal, W. L. Chan, J. M. Grimes, E. Manser, R. C. Robinson
An In Cellulo-Derived Structure Of Pak4 In Complex With Its Inhibitor Inka1
Nat Commun V. 6 8681 2015
PubMed-ID: 26607847  |  Reference-DOI: 10.1038/NCOMMS9681

(-) Compounds

Molecule 1 - PROTEIN FAM212A,SERINE/THREONINE-PROTEIN KINASE PAK 4
    Chains: A
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: CHLOROCEBUS AETHIOPS
    Expression System Cell: KIDNEY CELL CRL-1651
    Expression System Cell Line: COS-7
    Expression System Common: AFRICAN GREEN MONKEY
    Expression System Taxid: 9534
    Fragment: UNP RESIDUES 166-203,UNP RESIDUES 278-591
    Gene: FAM212A, C3ORF54, PAK4, KIAA1142
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: P21-ACTIVATED KINASE 4,PAK-4

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3SEP1Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:330 , SER A:331 , THR A:332 , VAL A:335 , LYS A:350 , MET A:395 , GLU A:396 , PHE A:397 , LEU A:398 , ASP A:440 , ASP A:458 , GLY A:460 , PHE A:461 , MG A:602 , MG A:603binding site for residue ATP A 601
2AC2SOFTWARESER A:331 , ATP A:601 , MG A:603binding site for residue MG A 602
3AC3SOFTWAREASP A:458 , ATP A:601 , MG A:602binding site for residue MG A 603

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XBR)

(-) 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:316
                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee....hhhhhh...hhhhhhhhhhhhhhh...hhhh.eeeeeeeee....eeeeeee.....eeeeeeee.....hhhhhhhhhhhhhhh.......eeeeeee..eeeeee.....eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee.hhhhhee...........eehhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh...........hhhhhhhhhhhh........hhhhhhhhhhhhhh.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xbr A 175 LNRGRSRQPLVLGDNCFADLVHNQRVSHEQFRAALQLVVDPGDPRSYLDNFIKIGEGSTGIVCIATVRSSGKLVAVKKMDLRKQQRRELLFNEVVIMRDYQHENVVEMYNSYLVGDELWVVMEFLEGGALTDIVTHTRMNEEQIAAVCLAVLQALSVLHAQGVIHRDIKSDSILLTHDGRVKLSDFGFCAQVSKEVPRRKsLVGTPYWMAPELISRLPYGPEVDIWSLGIMVIEMVDGEPPYFNEPPLKAMKMIRDNLPPRLKNLHKVSPSLKGFLDRLLVRDPAQRATAAELLKHPFLAKAGPPASIVPLMRQNR 589
                                   184       194  ||   303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473|      483       493       503       513       523       533       543       553       563       573       583      
                                                197|                                                                                                                                                                              474-SEP                                                                                                               
                                                 297
   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 4XBR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (27, 28)

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
    ATP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SEP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4xbr)
 

(-) 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
  4xbr
    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
  INKA1_HUMAN | Q96EL1
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  PAK4_HUMAN | O96013
    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)
  2.7.11.1
    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
  INKA1_HUMAN | Q96EL1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  PAK4_HUMAN | O96013
    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
        INKA1_HUMAN | Q96EL1: 4xbu
        PAK4_HUMAN | O96013: 2bva 2cdz 2j0i 2ov2 2q0n 2x4z 4app 4fie 4fif 4fig 4fih 4fii 4fij 4jdh 4jdi 4jdj 4jdk 4l67 4njd 4o0v 4o0x 4o0y 4xbu 5bms 5i0b

(-) Related Entries Specified in the PDB File

4xbu