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(-) Description

Title :  THE STRUCTURE OF IBUPROFEN BOUND TO CYCLOOXYGENASE-2
 
Authors :  B. J. Orlando, M. J. Lucido, M. G. Malkowski
Date :  05 May 14  (Deposition) - 26 Nov 14  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Membrane Protein, Cyclooxygenase, Cox, Cox-2, Ibuprofen, Monotopic, Prostaglandin, Nsaid, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. J. Orlando, M. J. Lucido, M. G. Malkowski
The Structure Of Ibuprofen Bound To Cyclooxygenase-2.
J. Struct. Biol. V. 189 62 2015
PubMed-ID: 25463020  |  Reference-DOI: 10.1016/J.JSB.2014.11.005

(-) Compounds

Molecule 1 - PROSTAGLANDIN G/H SYNTHASE 2
    ChainsA, B
    EC Number1.14.99.1
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Taxid7108
    FragmentUNP RESIDUES 20-568
    GenePTGS2, COX-2, COX2, PGHS-B, TIS10
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymCYCLOOXYGENASE-2,COX-2,GLUCOCORTICOID-REGULATED INFLAMMATORY CYCLOOXYGENASE,GRIPGHS,MACROPHAGE ACTIVATION-ASSOCIATED MARKER PROTEIN P71/73,PES-2,PHS II,PROSTAGLANDIN H2 SYNTHASE 2,PGHS-2, PROSTAGLANDIN-ENDOPEROXIDE SYNTHASE 2,TIS10 PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 34)

Asymmetric/Biological Unit (7, 34)
No.NameCountTypeFull Name
1AKR4Ligand/IonACRYLIC ACID
2BOG3Ligand/IonB-OCTYLGLUCOSIDE
3EDO13Ligand/Ion1,2-ETHANEDIOL
4HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
5IBP2Ligand/IonIBUPROFEN
6MAN1Ligand/IonALPHA-D-MANNOSE
7NAG9Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (30, 30)

Asymmetric Unit (30, 30)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:121 , VAL A:350 , TYR A:356 , GLY A:527 , ALA A:528 , SER A:531binding site for residue IBP A 601
02AC2SOFTWAREALA A:200 , GLN A:204 , HIS A:208 , PHE A:211 , LYS A:212 , THR A:213 , HIS A:215 , ASN A:383 , TYR A:386 , HIS A:387 , HIS A:389 , LEU A:392 , VAL A:448 , ALA A:451 , GLN A:455 , HOH A:818 , HOH A:993 , HOH A:998 , HOH A:1129binding site for residue HEM A 602
03AC3SOFTWAREGLU A:180 , ARG A:186 , ILE A:443 , GLN A:446 , HOH A:718 , GLU B:180 , LYS B:181 , ARG B:185 , ARG B:186 , ARG B:439 , GLU B:487 , GLU B:491binding site for residue BOG A 603
04AC4SOFTWARELYS A:83 , PRO A:84 , PRO A:86 , VAL A:89 , TRP A:100 , VAL A:117 , SER A:120 , ARG A:121 , HOH A:931 , HOH A:1213binding site for residue BOG A 604
05AC5SOFTWARESER A:478 , PHE A:479 , GLU A:480 , LYS A:493 , HOH A:1037binding site for residue AKR A 609
06AC6SOFTWAREARG A:241 , LYS A:244 , GLU A:273 , HOH A:1054 , HOH A:1192binding site for residue AKR A 610
07AC7SOFTWAREPRO A:163 , MET A:164 , LEU A:172 , ARG A:457 , LYS A:460 , TYR A:461 , HOH A:844binding site for residue EDO A 611
08AC8SOFTWAREGLU A:309 , ARG A:312 , GLU A:340 , SER A:567 , LEU A:568 , ASN A:571 , HOH A:712binding site for residue EDO A 612
09AC9SOFTWAREPRO A:548 , GLY A:553 , GLU A:554 , MET B:48binding site for residue EDO A 613
10AD1SOFTWARELYS A:252 , TYR A:255 , ASN A:311 , HOH A:945 , HOH A:981binding site for residue EDO A 614
11AD2SOFTWARESER A:144 , HOH A:893 , HOH A:897 , HOH A:911 , LEU B:225binding site for residue EDO A 615
12AD3SOFTWAREPHE A:210 , ASN A:376 , ILE A:378 , SER A:531 , GLY A:534 , HOH A:826 , HOH A:863 , HOH A:1200binding site for residue EDO A 616
13AD4SOFTWAREARG B:121 , VAL B:350 , TYR B:356 , GLY B:527 , ALA B:528 , SER B:531 , LEU B:532 , EDO B:618binding site for residue IBP B 601
14AD5SOFTWAREALA B:200 , GLN B:204 , HIS B:208 , PHE B:211 , LYS B:212 , THR B:213 , HIS B:215 , VAL B:296 , ASN B:383 , TYR B:386 , HIS B:387 , HIS B:389 , LEU B:392 , VAL B:448 , ALA B:451 , HOH B:823 , HOH B:918 , HOH B:1066binding site for residue HEM B 602
15AD6SOFTWARELYS B:83 , PRO B:84 , PRO B:86 , VAL B:89 , ILE B:92 , TYR B:116 , SER B:120 , ARG B:121 , HOH B:898 , HOH B:1057 , HOH B:1211 , HOH B:1252binding site for residue BOG B 603
16AD7SOFTWAREASP B:240 , ARG B:241 , LYS B:244 , VAL B:272 , GLU B:273binding site for residue AKR B 610
17AD8SOFTWARESER B:478 , PHE B:479 , GLU B:480 , LYS B:493 , HOH B:1277binding site for residue AKR B 611
18AD9SOFTWAREPRO B:163 , LEU B:172 , SER B:456 , ARG B:457 , LYS B:460 , TYR B:461 , HOH B:842binding site for residue EDO B 612
19AE1SOFTWAREGLU B:309 , ARG B:312 , GLU B:340 , SER B:567 , LEU B:568 , ASN B:571 , HOH B:792binding site for residue EDO B 613
20AE2SOFTWARELEU A:225 , SER B:144 , HOH B:865 , HOH B:936 , HOH B:980 , HOH B:1103binding site for residue EDO B 614
21AE3SOFTWAREPRO A:543 , HOH A:1163 , PHE B:372 , GLN B:373 , HOH B:912 , HOH B:1033 , HOH B:1122binding site for residue EDO B 615
22AE4SOFTWAREPHE B:210 , ASN B:376 , ILE B:378 , SER B:531 , GLY B:534 , EDO B:618 , HOH B:827 , HOH B:922binding site for residue EDO B 616
23AE5SOFTWAREGLY A:259 , GLY A:260 , CYS B:570 , ASN B:571 , VAL B:573 , HOH B:704binding site for residue EDO B 617
24AE6SOFTWAREPHE B:206 , TYR B:349 , TYR B:386 , SER B:531 , LEU B:535 , IBP B:601 , EDO B:616binding site for residue EDO B 618
25AE7SOFTWARETYR A:55 , GLU A:67 , ASN A:68 , HOH A:977 , HOH A:1068binding site for Mono-Saccharide NAG A 605 bound to ASN A 68
26AE8SOFTWAREGLU A:141 , ASN A:145 , TYR A:148 , ARG A:217 , PHE A:221 , HOH A:761 , HOH A:849 , HOH A:979 , HOH A:1208 , ASP B:240 , HOH B:951binding site for Poly-Saccharide residues NAG A 606 through NAG A 607 bound to ASN A 145
27AE9SOFTWAREGLN A:407 , ASN A:411 , SER A:413 , ILE A:414binding site for Mono-Saccharide NAG A 608 bound to ASN A 411
28AF1SOFTWARETYR B:55 , GLU B:67 , ASN B:68 , HOH B:988 , HOH B:1026binding site for Poly-Saccharide residues NAG B 604 through NAG B 605 bound to ASN B 68
29AF2SOFTWAREASP A:240 , GLU B:141 , ASN B:145 , TYR B:148 , ARG B:217 , HOH B:761 , HOH B:804 , HOH B:809 , HOH B:850binding site for Poly-Saccharide residues NAG B 606 through MAN B 608 bound to ASN B 145
30AF3SOFTWAREGLN B:407 , ASN B:411 , SER B:413 , ILE B:414 , GLU B:417binding site for Mono-Saccharide NAG B 609 bound to ASN B 411

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:36 -A:47
2A:37 -A:160
3A:41 -A:57
4A:59 -A:69
5A:570 -A:576
6B:36 -B:47
7B:37 -B:160
8B:41 -B:57
9B:59 -B:69
10B:570 -B:576

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:127 -Pro A:128
2Ser B:127 -Pro B:128

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PH9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PH9)

(-) Exons   (0, 0)

(no "Exon" information available for 4PH9)

(-) 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:551
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee..eeeee.....ee.....eehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...............hhhhhhh............................hhhhhhhhhh............hhhhhhhhhhhhh......................hhhhhh.hhhhhhhhh.........eee..eee..hhhhhh.........hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh..........hhhhhhhhhhhhhh...eee..eeehhhhhh.hhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh...hhhhhhhhh......hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ph9 A  33 HHPCCSNPCQNRGECMSTGFDQYKCDCTRTGFYGENCTTPEFLTRIKLLLKPTPNTVHYILTHFKGVWNIVNNIPFLRSLIMKYVLTSRSYLIDSPPTYNVHYGYKSWEAFSNLSYYTRALPPVADDCPTPMGVKGNKELPDSKEVLEKVLLRREFIPDPQGSNMMFAFFAQHFTHQFFKTDHKRGPGFTRGLGHGVDLNHIYGETLDRQHKLRLFKDGKLKYQVIGGEVYPPTVKDTQVEMIYPPHIPENLQFAVGQEVFGLVPGLMMYATIWLREHNRVCDILKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNQQFQYQNRIASEFNTLYHWHPLLPDTFNIEDQEYSFKQFLYNNSILLEHGLTQFVESFTRQIAGRVAGGRNVPIAVQAVAKASIDQSREMKYQSLNEYRKRFSLKPYTSFEELTGEKEMAAELKALYSDIDVMELYPALLVEKPRPDAIFGETMVELGAPFSLKGLMGNPICSPQYWKPSTFGGEVGFKIINTASIQSLICNNVKGCPFTSFNV 583
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582 

Chain B from PDB  Type:PROTEIN  Length:551
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeee.....eeee.....ee.....eehhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhh............................hhhhhhhhhh............hhhhhhhhhhhhh......................hhhhhh.hhhhhhhhh.........eee..eee..hhhhhh.........hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh..........hhhhhhhhhhhhhh...eee..eeehhhhhh..hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh...hhhhhhhhh......hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ph9 B  33 HHPCCSNPCQNRGECMSTGFDQYKCDCTRTGFYGENCTTPEFLTRIKLLLKPTPNTVHYILTHFKGVWNIVNNIPFLRSLIMKYVLTSRSYLIDSPPTYNVHYGYKSWEAFSNLSYYTRALPPVADDCPTPMGVKGNKELPDSKEVLEKVLLRREFIPDPQGSNMMFAFFAQHFTHQFFKTDHKRGPGFTRGLGHGVDLNHIYGETLDRQHKLRLFKDGKLKYQVIGGEVYPPTVKDTQVEMIYPPHIPENLQFAVGQEVFGLVPGLMMYATIWLREHNRVCDILKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNQQFQYQNRIASEFNTLYHWHPLLPDTFNIEDQEYSFKQFLYNNSILLEHGLTQFVESFTRQIAGRVAGGRNVPIAVQAVAKASIDQSREMKYQSLNEYRKRFSLKPYTSFEELTGEKEMAAELKALYSDIDVMELYPALLVEKPRPDAIFGETMVELGAPFSLKGLMGNPICSPQYWKPSTFGGEVGFKIINTASIQSLICNNVKGCPFTSFNV 583
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582 

   Legend:   → Mismatch (orange background)
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    → 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 4PH9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PH9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PH9)

(-) Gene Ontology  (85, 85)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        PGH2_MOUSE | Q057691cvu 1cx2 1dcx 1dd0 1ddx 1pxx 3hs5 3hs6 3hs7 3krk 3ln0 3ln1 3mdl 3mqe 3nt1 3ntb 3ntg 3olt 3olu 3pgh 3q7d 3qh0 3qmo 3rr3 3tzi 4cox 4e1g 4fm5 4m10 4m11 4otj 4oty 4rrw 4rrx 4rry 4rrz 4rs0 4rut 4z0l 5cox 5fdq 5jvy 5jvz 5jw1 6cox

(-) Related Entries Specified in the PDB File

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3nt1 HIGH RESOLUTION STRUCTURE OF NAPROXEN BOUND TO COX-2
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