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(-) Description

Title :  CRYSTAL STRUCTURE OF RIP1 KINASE IN COMPLEX WITH NECROSTATIN-3 ANALOG
 
Authors :  T. Xie, W. Peng, Y. Liu, C. Yan, Y. Shi
Date :  18 Jan 13  (Deposition) - 13 Mar 13  (Release) - 27 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.86
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha/Beta, Rip1 Kinase, Necroptosis, Necrostatins, Kinase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Xie, W. Peng, Y. Liu, C. Yan, J. Maki, A. Degterev, J. Yuan, Y. Shi
Structural Basis Of Rip1 Inhibition By Necrostatins.
Structure V. 21 493 2013
PubMed-ID: 23473668  |  Reference-DOI: 10.1016/J.STR.2013.01.016

(-) Compounds

Molecule 1 - RECEPTOR-INTERACTING SERINE/THREONINE-PROTEIN KINASE 1
    Chains: A, B
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Gene: RIPK1, RIP, RIP1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CELL DEATH PROTEIN RIP, RECEPTOR-INTERACTING PROTEIN 1, RIP- 1, SERINE/THREONINE-PROTEIN KINASE RIP

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
11HW2Ligand/Ion1-{(3S,3AS)-3-[3-FLUORO-4-(TRIFLUOROMETHOXY)PHENYL]-8-METHOXY-3,3A,4,5-TETRAHYDRO-2H-BENZO[G]INDAZOL-2-YL}-2-HYDROXYETHANONE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
11HW1Ligand/Ion1-{(3S,3AS)-3-[3-FLUORO-4-(TRIFLUOROMETHOXY)PHENYL]-8-METHOXY-3,3A,4,5-TETRAHYDRO-2H-BENZO[G]INDAZOL-2-YL}-2-HYDROXYETHANONE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
11HW1Ligand/Ion1-{(3S,3AS)-3-[3-FLUORO-4-(TRIFLUOROMETHOXY)PHENYL]-8-METHOXY-3,3A,4,5-TETRAHYDRO-2H-BENZO[G]INDAZOL-2-YL}-2-HYDROXYETHANONE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:45 , ALA A:64 , MET A:67 , VAL A:75 , VAL A:76 , LEU A:78 , LEU A:90 , MET A:92 , VAL A:134 , HIS A:136 , ILE A:154 , ALA A:155 , ASP A:156 , LEU A:157 , LEU A:159 , SER A:161 , PHE A:162BINDING SITE FOR RESIDUE 1HW A 301
2AC2SOFTWAREALA B:64 , MET B:67 , ASN B:68 , VAL B:75 , VAL B:76 , LEU B:78 , LEU B:90 , MET B:92 , VAL B:134 , HIS B:136 , ILE B:154 , ALA B:155 , ASP B:156 , LEU B:157 , SER B:161 , PHE B:162 , TRP B:165BINDING SITE FOR RESIDUE 1HW B 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ITI)

(-) 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:272
                                                                                                                                                                                                                                                                                                                
               SCOP domains d4itia_ A: automated matches                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee.............eeeee...eeeeeeeeee......hhhhhhhhhhhhh.........eeeeeee..eeeeee.....eehhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee........hhhhhhh.......hhhhh..hhhhh.......hhhhhhhhhhhhhhhhhh......hhhhhhhhhh............hhhhhhhhhhhh........hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iti A   8 NVIKMKSSDFLESAELDSGGFGKVSLAFHRTQGLMIMKTVYKGPNCIEHNEALLEEAKMMNRLRHSRVVKLLGVIIEEGKYSLVMEYMEKGNLMHVLKAEMSTPLSVKGRIILEIIEGMAYLHGKGVIHKDLKPENILVDNDFHIKIADLGLASFKMWSKLNNEEHNELGGTLYYMAPEHLNDVNAKPTEKSDVYSFAVVLWAIFANKEPYEQQLIMAIKSGNRPDVDDITEYCPREIISLMKLCWEANPEARPTFPGIEEKFRPFYLSQLE 294
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       187       197       207       217       227||     242       252       262       272       282       292  
                                                                                                                                                                                                  176|                                      228|                                                            
                                                                                                                                                                                                   187                                       234                                                            


Chain B from PDB  Type:PROTEIN  Length:270
                                                                                                                                                                                                                                                                                                              
               SCOP domains d4itib_ B: automated matches                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eehhh.ee.....eeeeee...eeeeeeeeee...hhhhhhhhhhhhhhhh.........eeeeeee..eeeeee.....eehhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee........hhhhhhhh.......hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh....hhhhh....hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4iti B   7 LNVIKMKSSDFLESAEKVSLAFHRTQGLMIMKTVYKGPNCIEHNEALLEEAKMMNRLRHSRVVKLLGVIIEEGKYSLVMEYMEKGNLMHVLKAEMSTPLSVKGRIILEIIEGMAYLHGKGVIHKDLKPENILVDNDFHIKIADLGLASFKMWSKLNNEEHNELGTLYYMAPEHLNDVNAKPTEKSDVYSFAVVLWAIFANKEPYENAIAEQQLIMAIKSGNRPDVDDITEYCPREIISLMKLCWEANPEARPTFPGIEEKFRPFYLSQLE 294
                                    16     || 33        43        53        63        73        83        93       103       113       123       133       143       153       163       173  ||   194       204       214       224       234       244       254       264       274       284       294
                                          22|                                                                                                                                               176|                                                                                                          
                                           30                                                                                                                                                188
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (75, 75)

Asymmetric Unit(hide GO term definitions)

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  4iti
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  RIPK1_HUMAN | Q13546
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  2.7.11.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        RIPK1_HUMAN | Q13546: 4ith 4itj 4neu 5hx6 5tx5

(-) Related Entries Specified in the PDB File

4ith 4itj