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 :  CRYSTAL STRUCTURE OF IRAK-4
 
Authors :  S. Johnstone, A. Sudom, J. Liu, N. P. Walker, Z. Wang
Date :  22 Oct 14  (Deposition) - 13 Jan 16  (Release) - 23 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Serine/Threonine Protein Kinase, Transferase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Johnstone, A. Sudom, J. Liu, N. P. Walker, Z. Wang
Crystal Structures Of Irak-4 Kinase In Complex With Inhibitors: A Serine/Threonine Kinase With Tyrosine As A Gatekeeper
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - INTERLEUKIN-1 RECEPTOR-ASSOCIATED KINASE 4
    Chains: A, B
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 154-460
    Gene: IRAK4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IRAK-4, RENAL CARCINOMA ANTIGEN NY-REN-64

 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, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1SEP2Mod. Amino AcidPHOSPHOSERINE
2T202Ligand/Ion3-NITRO-N-[1-PHENYL-5-(PIPERIDIN-1-YLMETHYL)-1H-BENZIMIDAZOL-2-YL]BENZAMIDE
3TPO3Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1SEP1Mod. Amino AcidPHOSPHOSERINE
2T201Ligand/Ion3-NITRO-N-[1-PHENYL-5-(PIPERIDIN-1-YLMETHYL)-1H-BENZIMIDAZOL-2-YL]BENZAMIDE
3TPO2Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1SEP1Mod. Amino AcidPHOSPHOSERINE
2T201Ligand/Ion3-NITRO-N-[1-PHENYL-5-(PIPERIDIN-1-YLMETHYL)-1H-BENZIMIDAZOL-2-YL]BENZAMIDE
3TPO1Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:185 , MET A:192 , VAL A:200 , ALA A:211 , LYS A:213 , TYR A:262 , VAL A:263 , TYR A:264 , MET A:265 , PRO A:266 , GLY A:268 , ARG A:273 , THR A:280 , LEU A:318 , HOH A:638BINDING SITE FOR RESIDUE T20 A 501
2AC2SOFTWAREMET B:192 , VAL B:200 , ALA B:211 , LYS B:213 , TYR B:262 , VAL B:263 , TYR B:264 , MET B:265 , PRO B:266 , THR B:280 , LEU B:318BINDING SITE FOR RESIDUE T20 B 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:392 -Pro A:393
2Glu B:392 -Pro B:393

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RMZ)

(-) 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:287
                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhh......hhhhh..eeee...eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee....ee......hhhhhhhhhhh.eehhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh...hhhhh........hhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rmz A 165 FHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASAQtVMtsRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMT 458
                                   174       184       194       204       214 ||    228       238       248       258       268       278       288       298       308       318       328       341|  ||  351       361       371       381       391       401       411       421       431       441       451       
                                                                             216|                                                                                                                336| |  ||                                                                                                                
                                                                              221                                                                                                                 340 |  ||                                                                                                                
                                                                                                                                                                                                    342-TPO                                                                                                                
                                                                                                                                                                                                       345-TPO                                                                                                             
                                                                                                                                                                                                        346-SEP                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:284
                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhhhhhhhh.............eeee...eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.........hhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.............hhhhhhhhh...hhhhh........hhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rmz B 165 FHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASVMtsRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMT 458
                                   174       184       194       204       214 ||    228       238       248       258       268       278       288       298       308       318       328       344||     354       364       374       384       394       404       414       424       434       444       454    
                                                                             216|                                                                                                                336| ||                                                                                                                
                                                                              221                                                                                                                 343 ||                                                                                                                
                                                                                                                                                                                                    345-TPO                                                                                                             
                                                                                                                                                                                                     346-SEP
   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 4RMZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (30, 30)

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
    SEP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    T20  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TPO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:392 - Pro A:393   [ RasMol ]  
    Glu B:392 - Pro B:393   [ 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
  4rmz
    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
  IRAK4_HUMAN | Q9NWZ3
    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
  IRAK4_HUMAN | Q9NWZ3
    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
        IRAK4_HUMAN | Q9NWZ3: 2nru 2nry 2o8y 2oib 2oic 2oid 3mop 4u97 4u9a 4xs2 4y73 4yo6 4yp8 4ztl 4ztm 4ztn 5kx7 5kx8 5t1s 5t1t 5uiq 5uir 5uis 5uit 5uiu

(-) Related Entries Specified in the PDB File

2nru 2nry