Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  THE STRUCTURE OF MECLOFENAMIC 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 :  2.41
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cox Meclofenamic, 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  (6, 20)

Asymmetric/Biological Unit (6, 20)
No.NameCountTypeFull Name
1AKR3Ligand/IonACRYLIC ACID
2BOG1Ligand/IonB-OCTYLGLUCOSIDE
3COH2Ligand/IonPROTOPORPHYRIN IX CONTAINING CO
4JMS2Ligand/Ion2-[(2,6-DICHLORO-3-METHYL-PHENYL)AMINO]BENZOIC ACID
5MAN4Ligand/IonALPHA-D-MANNOSE
6NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:179 , LYS A:180 , ARG A:184 , ARG A:185 , ARG A:438 , GLU A:486 , GLU A:490 , GLU B:180 , ARG B:185 , ARG B:186 , GLN B:446binding site for residue BOG A 601
02AC2SOFTWARETYR A:348 , VAL A:349 , LEU A:352 , SER A:353 , TYR A:355 , TYR A:385 , MET A:522 , GLY A:526 , ALA A:527 , SER A:530 , LEU A:531binding site for residue JMS A 602
03AC3SOFTWAREALA A:199 , ALA A:202 , GLN A:203 , HIS A:207 , PHE A:210 , LYS A:211 , THR A:212 , HIS A:214 , ASN A:382 , TYR A:385 , HIS A:386 , LEU A:391 , GLN A:454binding site for residue COH A 609
04AC4SOFTWAREARG A:240 , LYS A:243 , GLN A:270 , ALA A:271 , GLU A:272 , HOH A:833binding site for residue AKR A 610
05AC5SOFTWAREALA B:203 , GLN B:204 , HIS B:208 , PHE B:211 , LYS B:212 , THR B:213 , ASN B:383 , TYR B:386 , HIS B:387 , LEU B:392 , ALA B:451 , GLN B:455binding site for residue COH B 601
06AC6SOFTWARETYR B:349 , VAL B:350 , LEU B:353 , SER B:354 , TYR B:356 , TYR B:386 , MET B:523 , ALA B:528 , SER B:531 , LEU B:532binding site for residue JMS B 602
07AC7SOFTWAREARG B:241 , LYS B:244 , GLN B:271 , GLU B:273binding site for residue AKR B 609
08AC8SOFTWARELYS A:186 , ASN B:404 , TYR B:405 , GLN B:406binding site for residue AKR B 610
09AC9SOFTWARESER A:38 , TYR A:55 , GLU A:67 , ASN A:68binding site for Mono-Saccharide NAG A 603 bound to ASN A 68
10AD1SOFTWAREGLU A:140 , ASN A:144 , TYR A:147 , ARG A:216 , HOH A:711 , HOH A:796 , TYR B:65 , LEU B:239 , ARG B:243 , LYS B:244binding site for Poly-Saccharide residues NAG A 604 through MAN A 607 bound to ASN A 144
11AD2SOFTWAREGLN A:405 , GLN A:406 , ILE A:408 , ASN A:410binding site for Mono-Saccharide NAG A 608 bound to ASN A 410
12AD3SOFTWARESER B:38 , TYR B:55 , GLU B:67 , ASN B:68binding site for Mono-Saccharide NAG B 603 bound to ASN B 68
13AD4SOFTWARELEU A:238 , ARG A:242 , ASN B:145 , TYR B:148 , ARG B:217 , GLN B:558 , HOH B:751 , HOH B:842binding site for Poly-Saccharide residues NAG B 604 through MAN B 607 bound to ASN B 145
14AD5SOFTWAREGLN B:407 , ASN B:411 , SER B:413 , ILE B:414 , GLU B:417binding site for Mono-Saccharide NAG B 608 bound to ASN B 411

(-) 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: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:126 -Pro A:127
2Ser B:127 -Pro B:128

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IKQ)

(-) 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.....eehhhhhhhhhh..hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhh...............hhhhhhh............................hhhhhhhhhh............hhhhhhhhhhhhh......................hhhhhh.hhhhhhhhh.........eee..eee..hhhhhh.........hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh..........hhhhhhhhhhhhhh...eee..eeehhhhhh.hhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh...hhhhhhhhh......hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ikq 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...............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
                5ikq B   34 NPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILTHFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPDPQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVGQEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYHWHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGEKEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSVP  584
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583
   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 5IKQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (93, 93)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    AKR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    BOG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    COH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    JMS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MAN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
    AD5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ser A:126 - Pro A:127   [ RasMol ]  
    Ser B:127 - Pro B:128   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5ikq
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PGH2_HUMAN | P35354
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.14.99.1
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PGH2_HUMAN | P35354
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

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

(-) Related Entries Specified in the PDB File

5ikr 5ikt 5ikv