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(-) Description

Title :  THE STRUCTURE OF VIOXX BOUND TO HUMAN COX-2
 
Authors :  B. J. Orlando, M. G. Malkowski
Date :  16 Jun 16  (Deposition) - 28 Sep 16  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cyclooxyrgenase, Vioxx, Rofecoxib, Cox, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. J. Orlando, M. G. Malkowski
Crystal Structure Of Rofecoxib Bound To Human Cyclooxygenase-2.
Acta Crystallogr. , Sect. F V. 72 772 2016
PubMed-ID: 27710942  |  Reference-DOI: 10.1107/S2053230X16014230

(-) Compounds

Molecule 1 - PROSTAGLANDIN G/H SYNTHASE 2
    Chains: A, B
    EC Number: 1.14.99.1
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Gene: PTGS2, COX2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CYCLOOXYGENASE-2,COX-2,PHS II,PROSTAGLANDIN H2 SYNTHASE 2, PGHS-2,PROSTAGLANDIN-ENDOPEROXIDE SYNTHASE 2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 21)

Asymmetric/Biological Unit (7, 21)
No.NameCountTypeFull Name
1COH2Ligand/IonPROTOPORPHYRIN IX CONTAINING CO
2GOL1Ligand/IonGLYCEROL
3MAN2Ligand/IonALPHA-D-MANNOSE
4NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
5NH42Ligand/IonAMMONIUM ION
6PO46Ligand/IonPHOSPHATE ION
7RCX2Ligand/IonROFECOXIB

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:90 , GLN A:192 , VAL A:349 , LEU A:352 , SER A:353 , TYR A:355 , TRP A:387 , ARG A:513 , ALA A:516 , PHE A:518 , MET A:522 , VAL A:523 , ALA A:527 , SER A:530 , LEU A:531binding site for residue RCX A 601
02AC2SOFTWAREALA A:199 , GLN A:203 , HIS A:207 , PHE A:210 , THR A:212 , HIS A:214 , ASN A:382 , TYR A:385 , HIS A:386 , HIS A:388 , LEU A:391 , VAL A:447 , ALA A:450 , GLN A:454 , HOH A:703binding site for residue COH A 602
03AC3SOFTWAREASP A:515binding site for residue NH4 A 607
04AC4SOFTWARELYS A:83 , GLU A:524binding site for residue GOL A 608
05AC5SOFTWAREARG A:44 , VAL A:46 , ASP A:125 , TYR A:130 , LYS A:137 , HOH A:707binding site for residue PO4 A 609
06AC6SOFTWAREARG A:240 , LYS A:243 , GLN A:270 , ALA A:271 , GLU A:272binding site for residue PO4 A 610
07AC7SOFTWAREHIS A:351 , SER A:581binding site for residue PO4 A 611
08AC8SOFTWAREHIS B:90 , GLN B:192 , VAL B:349 , LEU B:352 , SER B:353 , TYR B:355 , ARG B:513 , ILE B:517 , PHE B:518 , MET B:522 , VAL B:523 , GLY B:526 , ALA B:527 , SER B:530binding site for residue RCX B 601
09AC9SOFTWAREALA B:199 , GLN B:203 , HIS B:207 , PHE B:210 , LYS B:211 , THR B:212 , HIS B:214 , ASN B:382 , TYR B:385 , HIS B:386 , HIS B:388 , LEU B:391 , VAL B:447 , GLN B:454 , HOH B:740binding site for residue COH B 602
10AD1SOFTWAREARG B:433 , ASP B:515binding site for residue NH4 B 607
11AD2SOFTWARELYS A:546 , ARG B:44 , VAL B:46 , ASP B:125 , TYR B:130 , LYS B:137binding site for residue PO4 B 608
12AD3SOFTWAREARG B:240 , LYS B:243 , GLN B:270 , ALA B:271 , GLU B:272binding site for residue PO4 B 609
13AD4SOFTWAREHIS B:351 , SER B:581binding site for residue PO4 B 610
14AD5SOFTWAREGLU A:140 , ASN A:144 , TYR A:147 , ARG A:216 , HOH A:717binding site for Poly-Saccharide residues NAG A 603 through MAN A 605 bound to ASN A 144
15AD6SOFTWAREGLN A:406 , ASN A:410 , SER A:412 , ILE A:413 , GLU A:416binding site for Mono-Saccharide NAG A 606 bound to ASN A 410
16AD7SOFTWARELEU A:238 , ALA A:239 , GLU B:140 , ASN B:144 , TYR B:147 , ARG B:216 , PHE B:220binding site for Poly-Saccharide residues NAG B 603 through MAN B 605 bound to ASN B 144
17AD8SOFTWAREGLN B:406 , ASN B:410 , ILE B:413 , GLU B:416binding site for Mono-Saccharide NAG B 606 bound to ASN B 410

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:36 -A:47
2A:37 -A:159
3A:41 -A:57
4A:59 -A:69
5A:569 -A:575
6B:36 -B:47
7B:37 -B:159
8B:41 -B:57
9B:59 -B:69
10B:569 -B:575

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:126 -Pro A:127
2Ser B:126 -Pro B:127

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KIR)

(-) 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 hhhhhh......eeee.....eeee.....ee.....eehhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......ee......hhhhhhh....ee......................hhhhhhhhhh............hhhhhhhhhhhhh......................hhhhhh.hhhhhhhhh.........eee..eee..hhhhhh.........hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh..........hhhhhhhhhhhhhh...eee..eeehhhhhh..hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh...hhhhhhhhh......hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5kir A   34 NPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILTHFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPDPQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVGQEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVNHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYHWHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGEKEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSVP  583
                                    43        53        63        73        83        93       103  |    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 
                                                                                                 105A                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:551
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh......eeee.....eeee.....ee.....eehhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhh............................hhhhhhhhhh............hhhhhhhhhhhhh......................hhhhhh.hhhhhhhhh.........eee..eee..hhhhhh.........hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh..........hhhhhhhhhhhhhh...eee..eeehhhhhh.hhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh...hhhhhhhhh......hhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5kir B   34 NPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILTHFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPDPQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVGQEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVNHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYHWHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGEKEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSVP  583
                                    43        53        63        73        83        93       103  |    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 
                                                                                                 105A
   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 5KIR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (93, 93)

Asymmetric/Biological Unit(hide GO term definitions)

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        PGH2_HUMAN | P35354: 1v0x 5f19 5f1a 5ikq 5ikr 5ikt 5ikv

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