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 CRYSTAL STRUCTURE OF SALICYLATE BOUND TO HUMAN CYCLOOXYGENASE-2
 
Authors :  M. J. Lucido, B. J. Orlando, M. G. Malkowski
Date :  30 Nov 15  (Deposition) - 16 Mar 16  (Release) - 16 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.38
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Membrane Protein, Monotopic, Cyclooxygenase, Cyclooxygenase-2, Cox, Pghs, Salicylic Acid, Salicylate, Inhibitor, Complex, Oxidoreductase-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Lucido, B. J. Orlando, A. J. Vecchio, M. G. Malkowski
Crystal Structure Of Aspirin-Acetylated Human Cyclooxygenase-2: Insight Into The Formation Of Products With Reversed Stereochemistry.
Biochemistry V. 55 1226 2016
PubMed-ID: 26859324  |  Reference-DOI: 10.1021/ACS.BIOCHEM.5B01378

(-) 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 Plasmid: PFASTBAC1
    Expression System Strain: SF21
    Expression System Taxid: 7108
    Gene: PTGS2, COX2
    Mutation: YES
    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, 23)

Asymmetric/Biological Unit (7, 23)
No.NameCountTypeFull Name
1AKR3Ligand/IonACRYLIC ACID
2BOG1Ligand/IonB-OCTYLGLUCOSIDE
3COH2Ligand/IonPROTOPORPHYRIN IX CONTAINING CO
4EDO5Ligand/Ion1,2-ETHANEDIOL
5MAN3Ligand/IonALPHA-D-MANNOSE
6NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE
7SAL2Ligand/Ion2-HYDROXYBENZOIC ACID

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:349 , LEU A:352 , TYR A:385 , TRP A:387 , MET A:522 , GLY A:526 , ALA A:527 , SER A:530 , EDO A:610 , HOH A:701binding site for residue SAL A 601
02AC2SOFTWARETYR A:148 , ALA A:199 , ALA A:202 , GLN A:203 , PHE A:210 , THR A:212 , HIS A:214 , ASN A:382 , TYR A:385 , HIS A:386 , HIS A:388 , LEU A:391 , GLN A:454binding site for residue COH A 602
03AC3SOFTWAREARG A:240 , LYS A:243 , GLU A:272binding site for residue AKR A 608
04AC4SOFTWAREGLU A:308 , ARG A:311 , GLU A:339 , SER A:566 , LEU A:567 , ASN A:570 , HOH A:702binding site for residue EDO A 609
05AC5SOFTWAREARG A:120 , TYR A:355 , SAL A:601binding site for residue EDO A 610
06AC6SOFTWAREPHE A:209 , ASN A:375 , ILE A:377 , SER A:530 , GLY A:533 , HOH A:703 , HOH A:720 , HOH A:727binding site for residue EDO A 611
07AC7SOFTWAREVAL B:349 , LEU B:384 , TYR B:385 , TRP B:387 , MET B:522 , GLY B:526 , ALA B:527 , SER B:530 , HOH B:702binding site for residue SAL B 601
08AC8SOFTWARETYR B:148 , ALA 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 , GLN B:454binding site for residue COH B 602
09AC9SOFTWAREGLU A:179 , ARG A:184 , ARG A:185 , GLN A:445 , GLU B:179 , ARG B:185 , ARG B:438 , GLU B:486 , GLU B:490binding site for residue BOG B 608
10AD1SOFTWAREARG B:240 , LYS B:243 , GLU B:272binding site for residue AKR B 609
11AD2SOFTWARELYS A:186 , ASN B:403 , TYR B:404 , GLN B:405binding site for residue AKR B 610
12AD3SOFTWAREARG B:311 , ILE B:558 , THR B:561 , ALA B:562 , SER B:566 , ASN B:570 , HOH B:701 , HOH B:840binding site for residue EDO B 611
13AD4SOFTWAREPHE B:209 , SER B:530 , GLY B:533 , LEU B:534 , HOH B:746 , HOH B:767binding site for residue EDO B 612
14AD5SOFTWAREGLU A:140 , ASN A:144 , TYR A:147 , ARG A:216 , GLN A:557 , HOH A:711 , HOH A:728 , HOH A:829 , LEU B:238 , ARG B:242binding site for Poly-Saccharide residues NAG A 603 through MAN A 606 bound to ASN A 144
15AD6SOFTWAREGLN A:406 , ASN A:410 , SER A:412 , ILE A:413 , GLU A:416 , HOH A:746 , HOH A:857binding site for Mono-Saccharide NAG A 607 bound to ASN A 410
16AD7SOFTWARETYR B:55 , GLU B:67 , ASN B:68 , HOH B:703binding site for Mono-Saccharide NAG B 603 bound to ASN B 68
17AD8SOFTWAREARG A:242 , GLU B:140 , ASN B:144 , TYR B:147 , ARG B:216 , HOH B:726 , HOH B:772binding site for Poly-Saccharide residues NAG B 604 through MAN B 606 bound to ASN B 144
18AD9SOFTWAREGLN B:406 , ILE B:408 , ASN B:410 , ILE B:413 , HOH B:709 , HOH B:803binding site for Mono-Saccharide NAG B 607 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 5F1A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F1A)

(-) Exons   (0, 0)

(no "Exon" information available for 5F1A)

(-) 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:553
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh......eeee.....eeee.....ee.....eehhhhhhhhhhh.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
                5f1a A   33 KNPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILTHFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPDPQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVGQEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYHWHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGEKEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSVPD  584
                                    42        52        62        72        82        92       102   |   111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581   
                                                                                                  105A                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:552
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhh......eeee.....eeee.....ee.....eehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.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
                5f1a B   33 KNPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILTHFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPDPQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVGQEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYHWHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGEKEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSVP  583
                                    42        52        62        72        82        92       102   |   111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581  
                                                                                                  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 5F1A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F1A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F1A)

(-) 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 ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MAN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SAL  [ 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 ]
    AD6  [ RasMol ]  +environment [ RasMol ]
    AD7  [ RasMol ]  +environment [ RasMol ]
    AD8  [ RasMol ]  +environment [ RasMol ]
    AD9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ser A:126 - Pro A:127   [ RasMol ]  
    Ser B:126 - Pro B:127   [ 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
  5f1a
    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 5ikq 5ikr 5ikt 5ikv 5kir

(-) Related Entries Specified in the PDB File

5f19