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(-) Description

Title :  CRYSTAL STRUCTURE OF MURINE IRE1 IN COMPLEX WITH OICR573 INHIBITOR
 
Authors :  M. Sanches, N. Duffy, M. Talukdar, N. Thevakumaran, D. Chiovitti, R. Al J. B. Patterson, F. Sicheri
Date :  16 May 14  (Deposition) - 03 Sep 14  (Release) - 10 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Schiff Base, Hydroxy Aryl Aldehydes (Haa), Inhibitor Complex, Unfolded Protein Response, Endoribonuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Sanches, N. M. Duffy, M. Talukdar, N. Thevakumaran, D. Chiovitti, M. D. Canny, K. Lee, I. Kurinov, D. Uehling, R. Al-Awar, G. Poda, M. Prakesch, B. Wilson, V. Tam, C. Schweitzer, A. Toro, J. L. Lucas, D. Vuga, L. Lehmann, D. Durocher, Q. Zeng, J. B. Patterson, F. Sicheri
Structure And Mechanism Of Action Of The Hydroxy-Aryl-Aldehyde Class Of Ire1 Endoribonuclease Inhibitors.
Nat Commun V. 5 4202 2014
PubMed-ID: 25164867  |  Reference-DOI: 10.1038/NCOMMS5202

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE/ENDORIBONUCLEASE IRE1
    ChainsB, A, C, D
    EC Number2.7.11.1, 3.1.26.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 550-977
    GeneERN1, IRE1
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymENDOPLASMIC RETICULUM-TO-NUCLEUS SIGNALING 1,INOSITOL- REQUIRING PROTEIN 1,IRE1-ALPHA,IRE1A

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
131L1Ligand/Ion3-METHOXY-5-METHYL-4'-(MORPHOLIN-4-YL)BIPHENYL-4-OL
2ADP4Ligand/IonADENOSINE-5'-DIPHOSPHATE
3MG4Ligand/IonMAGNESIUM ION
4PEU1Ligand/Ion2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56,59,62,65,68,71,74,77,80-HEPTACOSAOXADOOCTACONTAN-82-OL
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
131L1Ligand/Ion3-METHOXY-5-METHYL-4'-(MORPHOLIN-4-YL)BIPHENYL-4-OL
2ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
4PEU1Ligand/Ion2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56,59,62,65,68,71,74,77,80-HEPTACOSAOXADOOCTACONTAN-82-OL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
131L-1Ligand/Ion3-METHOXY-5-METHYL-4'-(MORPHOLIN-4-YL)BIPHENYL-4-OL
2ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
4PEU-1Ligand/Ion2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56,59,62,65,68,71,74,77,80-HEPTACOSAOXADOOCTACONTAN-82-OL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS B:579 , GLY B:580 , ALA B:581 , VAL B:586 , LYS B:599 , GLU B:643 , CYS B:645 , HIS B:692 , ASN B:693 , LEU B:695 , ASP B:711 , MG B:1002binding site for residue ADP B 1001
02AC2SOFTWAREHIS B:692 , ASN B:693 , ASP B:711 , ADP B:1001binding site for residue MG B 1002
03AC3SOFTWAREGLY A:578 , GLY A:580 , THR A:584 , ALA A:597 , LYS A:599 , ILE A:642 , CYS A:645 , THR A:648 , HIS A:692 , ASN A:693 , LEU A:695 , ASP A:711 , MG A:1003binding site for residue ADP A 1002
04AC4SOFTWAREHIS A:692 , ASN A:693 , ASP A:711 , ADP A:1002binding site for residue MG A 1003
05AC5SOFTWARETYR A:772 , HIS A:773 , GLY A:776 , LYS A:777 , SER A:778 , ARG A:781 , 31L A:1001 , LEU C:787binding site for residue PEU A 1004
06AC6SOFTWARELEU C:577 , HIS C:579 , GLY C:580 , VAL C:586 , ALA C:597 , LYS C:599 , GLU C:643 , CYS C:645 , LYS C:690 , HIS C:692 , ASN C:693 , LEU C:695 , MG C:1002binding site for residue ADP C 1001
07AC7SOFTWAREASN C:693 , ASP C:711 , ADP C:1001binding site for residue MG C 1002
08AC8SOFTWARELEU D:577 , GLY D:578 , HIS D:579 , GLY D:580 , LYS D:599 , GLU D:643 , LYS D:690 , HIS D:692 , ASN D:693 , LEU D:695 , ASP D:711 , MG D:1002binding site for residue ADP D 1001
09AC9SOFTWAREHIS D:692 , ASN D:693 , ASP D:711 , ADP D:1001binding site for residue MG D 1002
10AD1SOFTWAREGLN A:655 , TYR A:772 , PHE A:889 , TYR A:892 , ALA A:903 , MET A:904 , ARG A:905 , ASN A:906 , LYS A:908 , HIS A:909 , HIS A:910 , TYR A:911 , PEU A:1004binding site for Di-peptide 31L A 1001 and LYS A 907

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PL5)

(-) Cis Peptide Bonds  (24, 24)

Asymmetric Unit
No.Residues
1Gly B:567 -Lys B:568
2His B:660 -Leu B:661
3Leu B:661 -Gly B:662
4Phe B:775 -Gly B:776
5Arg B:890 -Thr B:891
6Ile B:925 -Pro B:926
7His A:660 -Leu A:661
8Leu A:661 -Gly A:662
9Phe A:775 -Gly A:776
10Arg A:890 -Thr A:891
11Gly A:923 -Ser A:924
12Ile A:925 -Pro A:926
13Gly C:567 -Lys C:568
14Leu C:661 -Gly C:662
15Phe C:775 -Gly C:776
16Arg C:890 -Thr C:891
17Gly C:923 -Ser C:924
18Ile C:925 -Pro C:926
19Gly D:567 -Lys D:568
20Leu D:661 -Gly D:662
21Phe D:775 -Gly D:776
22Arg D:890 -Thr D:891
23Gly D:923 -Ser D:924
24Ile D:925 -Pro D:926

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PL5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PL5)

(-) Exons   (0, 0)

(no "Exon" information available for 4PL5)

(-) 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:386
                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeee.hhh.eeeeee....eeeeee.....eeehhhhhhhhhhh........eeeee......eeeee...eehhhhhhhh.......hhhhhhhhhhhhhhhhhhh...........eee..........eee....eee...........hhhhh...hhhhhhhhhhhhhhhhh..........hhhhhhhhh..........hhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pl5 A 562 RMVIVGKISFCPKDVLGHGAEGTIVYKGMFDNRDVAVKRILPECFSFADREVQLLRESDEHPNVIRYFCTEKDRQFQYIAIELCAATLQEYVEQKDFAHLGLEPITLLHQTTSGLAHLHSLNIVHRDLKPHNILLSMPNAHGRIKAMISDFGLCKKLVPGTEGWIAPEMLSEPTYTVDIFSAGCVFYYVISEGYHPFGKSLQRQANILLGACNLDCFHSDKHEDVIARELIEKMIAMDPQQRPSAKHVLKHPFFWSLEKQLQFFQDVSDRIEKEALDGPIVRQLERGGRAVVKMDWRENITVPLQTDLRKFRTYKGGSVRDLLRAMRNKKHHYRELPVEVQETLGSIPDDFVRYFTSRFPHLLSHTYQAMELCRHERLFQTYYWHE 964
                                   571       581       591       601       611       621       631       641       651       661       671       681       691       701       711      |733       743 ||    758       768       778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958      
                                                                                                                                                                                      718|           745|                                                                                                                                                                                                                     
                                                                                                                                                                                       731            751                                                                                                                                                                                                                     

Chain B from PDB  Type:PROTEIN  Length:383
                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeee.....eeeeee....eeeeeee....eeehhhhhhhhhh.........eeeee.....eeeeee.eeeehhhhhhh........hhhhhhhhhhhhhhhhhhh.......hhh.eeee.........eee....eee.........hhhhh...hhhhhhhhhhhhhhhhh..........hhhhhhhhh..........hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh..hhhhhh.hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pl5 B 562 RMVIVGKISFCPKDVLGHGAEGTIVYKGMFDNRDVAVKRILPECFSFADREVQLLRESDEHPNVIRYFCTEKDRQFQYIAIELCAATLQEYVEQKDFAHLGLEPITLLHQTTSGLAHLHSLNIVHRDLKPHNILLSMPNAHGRIKAMISDFGLCKKVPGTEGWIAPEMLSPTYTVDIFSAGCVFYYVISEGYHPFGKSLQRQANILLGACNLDCFHSDKHEDVIARELIEKMIAMDPQQRPSAKHVLKHPFFWSLEKQLQFFQDVSDRIEKEALDGPIVRQLERGGRAVVKMDWRENITVPLQTDLRKFRTYKGGSVRDLLRAMRNKKHHYRELPVEVQETLGSIPDDFVRYFTSRFPHLLSHTYQAMELCRHERLFQTYYWH 963
                                   571       581       591       601       611       621       631       641       651       661       671       681       691       701       711     ||734       744|      760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960   
                                                                                                                                                                                     717|          744|                                                                                                                                                                                                                    
                                                                                                                                                                                      731           751                                                                                                                                                                                                                    

Chain C from PDB  Type:PROTEIN  Length:386
                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeee.....eeeeee....eeeeeee.......hhhhhhhhhh.........eeeee.....eeeee..eeeehhhhhhh........hhhhhhhhhhhhhhhhhhh.......hhh.eeee.........eee..................hhhhh...hhhhhhhhhhhhhhhhhh..........hhhhhhhhh..........hhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh...............hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pl5 C 562 RMVIVGKISFCPKDVLGHGAEGTIVYKGMFDNRDVAVKRILPECFSFADREVQLLRESDEHPNVIRYFCTEKDRQFQYIAIELCAATLQEYVEQKDFAHLGLEPITLLHQTTSGLAHLHSLNIVHRDLKPHNILLSMPNAHGRIKAMISDFGLCKKLAVPGTEGWIAPEMLSNPTYTVDIFSAGCVFYYVISEGYHPFGKSLQRQANILLGACNLDCFHSDKHEDVIARELIEKMIAMDPQQRPSAKHVLKHPFFWSLEKQLQFFQDVSDRIEKEALDGPIVRQLERGGRAVVKMDWRENITVPLQTDLRKFRTYKGGSVRDLLRAMRNKKHHYRELPVEVQETLGSIPDDFVRYFTSRFPHLLSHTYQAMELCRHERLFQTYYWH 963
                                   571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       732       742 ||    757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907       917       927       937       947       957      
                                                                                                                                                                                       719|          744|                                                                                                                                                                                                                     
                                                                                                                                                                                        731           750                                                                                                                                                                                                                     

Chain D from PDB  Type:PROTEIN  Length:385
                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeee.hhh.eeeeee....eeeeeee....ee.hhhhhhhhhh.........eeeee.....eeeee....eehhhhhhh........hhhhhhhhhhhhhhhhhhh...........eee..........eee.....ee..........hhhhh...hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh..........hhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.........hhhhh.hhhhhhhhh........hhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhh......hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pl5 D 561 TRMVIVGKISFCPKDVLGHGAEGTIVYKGMFDNRDVAVKRILPECFSFADREVQLLRESDEHPNVIRYFCTEKDRQFQYIAIELCAATLQEYVEQKDFAHLGLEPITLLHQTTSGLAHLHSLNIVHRDLKPHNILLSMPNAHGRIKAMISDFGLCKKLVPGTEGWIAPEMLSPTYTVDIFSAGCVFYYVISEGYHPFGKSLQRQANILLGACNLDCFHSDKHEDVIARELIEKMIAMDPQQRPSAKHVLKHPFFWSLEKQLQFFQDVSDRIEKEALDGPIVRQLERGGRAVVKMDWRENITVPLQTDLRKFRTYKGGSVRDLLRAMRNKKHHYRELPVEVQETLGSIPDDFVRYFTSRFPHLLSHTYQAMELCRHERLFQTYYWH 963
                                   570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       732       742 ||    758       768       778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958     
                                                                                                                                                                                       718|          744|                                                                                                                                                                                                                    
                                                                                                                                                                                        731           751                                                                                                                                                                                                                    

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4PL5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PL5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PL5)

(-) Gene Ontology  (59, 59)

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  Cis Peptide Bonds
    Arg A:890 - Thr A:891   [ RasMol ]  
    Arg B:890 - Thr B:891   [ RasMol ]  
    Arg C:890 - Thr C:891   [ RasMol ]  
    Arg D:890 - Thr D:891   [ RasMol ]  
    Gly A:923 - Ser A:924   [ RasMol ]  
    Gly B:567 - Lys B:568   [ RasMol ]  
    Gly C:567 - Lys C:568   [ RasMol ]  
    Gly C:923 - Ser C:924   [ RasMol ]  
    Gly D:567 - Lys D:568   [ RasMol ]  
    Gly D:923 - Ser D:924   [ RasMol ]  
    His A:660 - Leu A:661   [ RasMol ]  
    His B:660 - Leu B:661   [ RasMol ]  
    Ile A:925 - Pro A:926   [ RasMol ]  
    Ile B:925 - Pro B:926   [ RasMol ]  
    Ile C:925 - Pro C:926   [ RasMol ]  
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    Leu A:661 - Gly A:662   [ RasMol ]  
    Leu B:661 - Gly B:662   [ RasMol ]  
    Leu C:661 - Gly C:662   [ RasMol ]  
    Leu D:661 - Gly D:662   [ RasMol ]  
    Phe A:775 - Gly A:776   [ RasMol ]  
    Phe B:775 - Gly B:776   [ RasMol ]  
    Phe C:775 - Gly C:776   [ RasMol ]  
    Phe D:775 - Gly D:776   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        ERN1_MOUSE | Q9EQY04pl3 4pl4

(-) Related Entries Specified in the PDB File

4pl3 4PL3 CONTAINS THE SAME PROTEIN COMPLEX WITH ANOTHER INHIBITOR (MKC9989)
4pl4 4PL4 CONTAINS THE SAME PROTEIN COMPLEX WITH ANOTHER INHIBITOR (OICR464)