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(-) Description

Title :  THE STRUCTURE OF TOLFENAMIC ACID BOUND TO HUMAN CYCLOOXYGENASE-2
 
Authors :  B. J. Orlando, M. G. Malkowski
Date :  03 Mar 16  (Deposition) - 25 May 16  (Release) - 27 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cox Tolfenamic, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. J. Orlando, M. G. Malkowski
Substrate-Selective Inhibition Of Cyclooxygeanse-2 By Fenamic Acid Derivatives Is Dependent On Peroxide Tone.
J. Biol. Chem. V. 291 15069 2016
PubMed-ID: 27226593  |  Reference-DOI: 10.1074/JBC.M116.725713

(-) 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  (5, 21)

Asymmetric/Biological Unit (5, 21)
No.NameCountTypeFull Name
1COH2Ligand/IonPROTOPORPHYRIN IX CONTAINING CO
2MAN2Ligand/IonALPHA-D-MANNOSE
3NAG9Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PO46Ligand/IonPHOSPHATE ION
5TLF2Ligand/Ion2-[(3-CHLORO-2-METHYLPHENYL)AMINO]BENZOIC ACID

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:349 , LEU A:352 , TYR A:355 , TYR A:385 , MET A:522 , GLY A:526 , ALA A:527 , SER A:530 , LEU A:531 , HOH A:735binding site for residue TLF A 601
02AC2SOFTWARETYR A:148 , ALA A:199 , GLN A:203 , HIS A:207 , PHE A:210 , THR A:212 , HIS A:214 , VAL A:295 , ASN A:382 , TYR A:385 , HIS A:386 , HIS A:388 , LEU A:391 , ALA A:450 , GLN A:454 , HOH A:719binding site for residue COH A 602
03AC3SOFTWAREARG A:240 , LYS A:243 , GLN A:270 , ALA A:271 , GLU A:272binding site for residue PO4 A 608
04AC4SOFTWAREARG A:44 , VAL A:46 , ASP A:125 , TYR A:130 , LYS A:137binding site for residue PO4 A 609
05AC5SOFTWAREARG A:433 , ASP A:515binding site for residue PO4 A 610
06AC6SOFTWAREVAL B:349 , TYR B:355 , TYR B:385 , TRP B:387 , MET B:522 , VAL B:523 , GLY B:526 , ALA B:527 , SER B:530 , HOH B:804binding site for residue TLF B 601
07AC7SOFTWAREALA B:199 , GLN B:203 , HIS B:207 , PHE B:210 , THR B:212 , VAL B:295 , ASN B:382 , TYR B:385 , HIS B:386 , HIS B:388 , LEU B:391 , VAL B:447 , GLN B:454 , HOH B:810binding site for residue COH B 602
08AC8SOFTWAREARG B:240 , LYS B:243 , ALA B:271binding site for residue PO4 B 609
09AC9SOFTWAREARG B:44 , VAL B:46 , ASP B:125 , TYR B:130 , LYS B:137 , HOH B:789binding site for residue PO4 B 610
10AD1SOFTWAREARG B:433 , ASP B:515binding site for residue PO4 B 611
11AD2SOFTWAREGLU A:140 , ASN A:144 , TYR A:147 , ARG A:216 , HOH A:751 , HOH A:756 , LEU B:238 , ARG B:242binding site for Poly-Saccharide residues NAG A 603 through MAN A 605 bound to ASN A 144
12AD3SOFTWAREGLN A:406 , ASN A:410 , SER A:412 , ILE A:413 , GLU A:416binding site for Poly-Saccharide residues NAG A 606 through NAG A 607 bound to ASN A 410
13AD4SOFTWARETYR B:55 , GLU B:67 , ASN B:68binding site for Mono-Saccharide NAG B 603 bound to ASN B 68
14AD5SOFTWARELEU A:238 , ARG A:242 , GLU B:140 , ASN B:144 , TYR B:147 , ARG B:216 , PHE B:220 , HOH B:750 , HOH B:787 , HOH B:797binding site for Poly-Saccharide residues NAG B 604 through MAN B 606 bound to ASN B 144
15AD6SOFTWAREGLN B:406 , ASN B:410 , SER B:412 , ILE B:413 , GLU B:416binding site for Poly-Saccharide residues NAG B 607 through NAG B 608 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 5IKT)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IKT)

(-) 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......eeeee...eeeee.....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
                5ikt A   34 NPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILTHFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPDPQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVGQEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYHWHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGEKEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSVP  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......eeeee...eeeee.....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
                5ikt B   34 NPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILTHFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPDPQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVGQEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYHWHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGEKEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSVP  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 5IKT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (93, 93)

Asymmetric/Biological Unit(hide GO term definitions)

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  5ikt
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 Related Entries

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

UniProtKB/Swiss-Prot
        PGH2_HUMAN | P35354: 1v0x 5f19 5f1a 5ikq 5ikr 5ikv 5kir

(-) Related Entries Specified in the PDB File

5ikq 5ikr 5ikv