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(-) Description

Title :  STRUCTURE OF INACTIVE KINASE RIP2K(K47R)
 
Authors :  E. Pellegrini, S. Cusack
Date :  16 Mar 17  (Deposition) - 28 Jun 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  D  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A  (1x)
Biol. Unit 4:  C  (1x)
Keywords :  Rip2K, Kinase, Inactive State, Helixc-Out, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Pellegrini, L. Signor, S. Singh, E. Boeri Erba, S. Cusack
Structures Of The Inactive And Active States Of Rip2 Kinase Inform On The Mechanism Of Activation.
Plos One V. 12 77161 2017
PubMed-ID: 28545134  |  Reference-DOI: 10.1371/JOURNAL.PONE.0177161

(-) Compounds

Molecule 1 - RECEPTOR-INTERACTING SERINE/THREONINE-PROTEIN KINASE 2
    Chains: D, A
    EC Number: 2.7.11.1, 2.7.10.2
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Gene: RIPK2, CARDIAK, RICK, RIP2, UNQ277/PRO314/PRO34092
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CARD-CONTAINING INTERLEUKIN-1 BETA-CONVERTING ENZYME- ASSOCIATED KINASE,CARD-CONTAINING IL-1 BETA ICE-KINASE,RIP-LIKE- INTERACTING CLARP KINASE,RECEPTOR-INTERACTING PROTEIN 2,RIP-2, TYROSINE-PROTEIN KINASE RIPK2
 
Molecule 2 - RECEPTOR-INTERACTING SERINE/THREONINE-PROTEIN KINASE 2
    Chains: B, C
    EC Number: 2.7.11.1, 2.7.10.2
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Gene: RIPK2, CARDIAK, RICK, RIP2, UNQ277/PRO314/PRO34092
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CARD-CONTAINING INTERLEUKIN-1 BETA-CONVERTING ENZYME- ASSOCIATED KINASE,CARD-CONTAINING IL-1 BETA ICE-KINASE,RIP-LIKE- INTERACTING CLARP KINASE,RECEPTOR-INTERACTING PROTEIN 2,RIP-2, TYROSINE-PROTEIN KINASE RIPK2

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x):    D
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x): A   
Biological Unit 4 (1x):   C 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 24)

Asymmetric Unit (2, 24)
No.NameCountTypeFull Name
1SO422Ligand/IonSULFATE ION
2TPO2Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION
2TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 2 (1, 7)
No.NameCountTypeFull Name
1SO47Ligand/IonSULFATE ION
2TPO-1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 3 (2, 5)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
2TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 4 (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
2TPO-1Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER B:282 , LEU B:284 , PRO D:281 , SER D:282 , LYS D:285 , HOH D:508binding site for residue SO4 D 401
02AC2SOFTWAREGLY D:27 , ALA D:28 , SER D:29 , ARG D:47 , LYS D:148 , HOH D:501binding site for residue SO4 D 402
03AC3SOFTWARESER A:271 , LYS A:285 , HIS D:16 , LYS D:17 , ALA D:38 , ASP D:39binding site for residue SO4 D 403
04AC4SOFTWAREVAL D:32 , TYR D:97 , MET D:98 , LEU D:153binding site for residue SO4 D 404
05AC5SOFTWAREVAL D:32 , ARG D:47 , LEU D:79 , THR D:95 , ASP D:164 , SO4 D:406binding site for residue SO4 D 405
06AC6SOFTWARELEU D:79 , ILE D:81 , ILE D:93 , ALA D:163 , ASP D:164 , PHE D:165 , SO4 D:405binding site for residue SO4 D 406
07AC7SOFTWAREGLY B:27 , ALA B:28 , SER B:29 , ARG B:47 , LYS B:148binding site for residue SO4 B 401
08AC8SOFTWAREILE B:250 , ARG B:262binding site for residue SO4 B 402
09AC9SOFTWAREPRO B:281 , SER B:282 , LYS B:285 , HOH B:504 , SER D:282 , HOH D:506binding site for residue SO4 B 403
10AD1SOFTWAREALA B:19 , ASP B:20 , ALA C:263 , ARG C:264binding site for residue SO4 B 404
11AD2SOFTWARELEU B:24 , TYR B:97 , MET B:98binding site for residue SO4 B 405
12AD3SOFTWAREVAL B:32 , ARG B:47 , THR B:95 , ALA B:163 , ASP B:164binding site for residue SO4 B 406
13AD4SOFTWAREALA B:19 , ASP B:20 , ARG B:36 , ARG C:264 , GLU C:289binding site for residue SO4 B 407
14AD5SOFTWAREGLY A:27 , ALA A:28 , SER A:29 , ARG A:47 , ASP A:146 , LYS A:148binding site for residue SO4 A 401
15AD6SOFTWAREILE A:250 , ASN A:251 , ARG A:262 , SO4 A:403binding site for residue SO4 A 402
16AD7SOFTWAREILE A:266 , GLU A:270 , SO4 A:402binding site for residue SO4 A 403
17AD8SOFTWAREGLU A:66 , LEU A:70 , GLY A:166binding site for residue SO4 A 404
18AD9SOFTWARESER A:282 , LEU A:284 , SER C:282 , LEU C:284binding site for residue SO4 C 401
19AE1SOFTWAREGLY C:27 , ALA C:28 , SER C:29 , ARG C:47 , LYS C:148binding site for residue SO4 C 402
20AE2SOFTWAREHIS B:16 , LYS B:17 , ALA B:38 , ASP B:39 , SER C:271 , PRO C:281 , LYS C:285binding site for residue SO4 C 403
21AE3SOFTWARELEU C:24 , MET C:98binding site for residue SO4 C 404
22AE4SOFTWAREILE C:250 , ASN C:251 , ARG C:262binding site for residue SO4 C 405
23AE5SOFTWAREHIS A:145 , MET A:172 , PRO A:200 , GLY A:201 , LYS A:203 , SER A:204 , ALA A:206 , SER A:207 , PHE A:229 , GLU A:230 , VAL A:232 , THR A:233 , PHE C:229 , GLU C:230 , VAL C:232 , THR C:233binding site for Di-peptide ARG A 205 and ASP C 231

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5NG3)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Thr D:139 -Pro D:140
2Thr B:139 -Pro B:140
3Thr A:139 -Pro A:140
4Thr C:139 -Pro C:140

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5NG3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5NG3)

(-) Exons   (0, 0)

(no "Exon" information available for 5NG3)

(-) 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:284
                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhh.eeeeeeeeee..eeeeeeee.....eeeeeeee.....hhhhhhhhhhhhhhhhh........eeeeeee..eeeeeee.....hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh..............eee.....eee....hhhhhhhhhhh..........hhhhhh...hhhhh.hhhhhhhhhhhhhhhhh........hhhhhhhhhhh................hhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ng3 A   8 SALPTIPYHKLADLRYLSRGASGTVSSARHADWRVQVAVRHLHIHTPLLDSERKDVLREAEILHKARFSYILPILGICNEPEFLGIVTEYMPNGSLNELLHRKtEYPDVAWPLRFRILHEIALGVNYLHNMTPPLLHHDLKTQNILLDNEFHVKIADFGLSKWRMMSLSQSREGGTIIYMPPENYEPGQKSRASIKHDIYSYAVITWEVLSRKQPFEDVTNPLQIMYSVSQGHRPVINEESLPYDIPHRARMISLIESGWAQNPDERPSFLKCLIELEPVLRTF 297
                                    17        27        37        47        57        67        77        87        97       107   |   117       127       137       147       157       167       177 ||    193       203       213       223       233       243       253       263       273       283       293    
                                                                                                                                 111-TPO                                                             179|                                                                                                               
                                                                                                                                                                                                      186                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:275
                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhh.eeeeeeeeee..eeeeeeee.....eeeeeeee.....hhhhhhhhhhhhhhhhh........eeeeeee..eeeeeee.....hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh..............eee.....eee....hhhhhhhhhhh........hhhhhh...hhhhhhhhhhhhhhhhh........hhhhhhhhhhh................hhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ng3 B   9 ALPTIPYHKLADLRYLSRGASGTVSSARHADWRVQVAVRHLHIHTPLLDSERKDVLREAEILHKARFSYILPILGICNEPEFLGIVTEYMPNGSLNELLHRKTEYPDVAWPLRFRILHEIALGVNYLHNMTPPLLHHDLKTQNILLDNEFHVKIADFGLSKWRMMSLSQSGGTIIYMPPENYEPSIKHDIYSYAVITWEVLSRKQPFEDVTNPLQIMYSVSQGHRPVINEESLPYDIPHRARMISLIESGWAQNPDERPSFLKCLIELEPVLRTF 297
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178|      196   ||  212       222       232       242       252       262       272       282       292     
                                                                                                                                                                                                   178|          200|                                                                                          
                                                                                                                                                                                                    187           207                                                                                          


Chain C from PDB  Type:PROTEIN  Length:272
                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhh.eeeeeeeeee..eeeeeeee.....eeeeeeee.....hhhhhhhhhhhhhhhhh........eeeeeee..eeeeeee.....hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh..............eee.....eee....hhhhhhhhhhh.......hhhhh..hhhhhhhhhhhhhhhhh........hhhhhhhhhhh................hhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ng3 C   9 ALPTIPYHKLADLRYLSRGASGTVSSARHADWRVQVAVRHLHIHTPLLDSERKDVLREAEILHKARFSYILPILGICNEPEFLGIVTEYMPNGSLNELLHRKTEYPDVAWPLRFRILHEIALGVNYLHNMTPPLLHHDLKTQNILLDNEFHVKIADFGLSKWRMMSLSQSGTIIYMPPENYSIKHDIYSYAVITWEVLSRKQPFEDVTNPLQIMYSVSQGHRPVINEESLPYDIPHRARMISLIESGWAQNPDERPSFLKCLIELEPVLRTF 297
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178|      197||     215       225       235       245       255       265       275       285       295  
                                                                                                                                                                                                   178|       198|                                                                                          
                                                                                                                                                                                                    188        207                                                                                          


Chain D from PDB  Type:PROTEIN  Length:279
                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhh.eeeeeeeeee..eeeeeeee.....eeeeeeee.....hhhhhhhhhhhhhhhhh........eeeeeee..eeeeeee.....hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh..............eee.....eee....hhhhhhhhhhh..........hhhhhh.....hhhhhhhhhhhhhhhhh........hhhhhhhhhhh................hhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ng3 D   9 ALPTIPYHKLADLRYLSRGASGTVSSARHADWRVQVAVRHLHIHTPLLDSERKDVLREAEILHKARFSYILPILGICNEPEFLGIVTEYMPNGSLNELLHRKtEYPDVAWPLRFRILHEIALGVNYLHNMTPPLLHHDLKTQNILLDNEFHVKIADFGLSKWRMMSLSQSREGGTIIYMPPENYEPRASIKHDIYSYAVITWEVLSRKQPFEDVTNPLQIMYSVSQGHRPVINEESLPYDIPHRARMISLIESGWAQNPDERPSFLKCLIELEPVLRTF 297
                                    18        28        38        48        58        68        78        88        98       108  |    118       128       138       148       158       168       178||     194     ||208       218       228       238       248       258       268       278       288         
                                                                                                                                111-TPO                                                             179|           200|                                                                                            
                                                                                                                                                                                                     186            205
   Legend:   → Mismatch (orange background)
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  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 5NG3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5NG3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5NG3)

(-) Gene Ontology  (74, 74)

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  5ng3
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  RIPK2_HUMAN | O43353
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RIPK2_HUMAN | O43353: 2n7z 2n83 4c8b 5ar2 5ar3 5ar4 5ar5 5ar7 5ar8 5j79 5j7b 5ng0 5ng2

(-) Related Entries Specified in the PDB File

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