Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM DIHYDROOROTATE DEHYDROGENASE BOUND WITH INHIBITOR DSM265
 
Authors :  M. Phillips, X. Deng, D. Tomchick
Date :  27 May 15  (Deposition) - 29 Jul 15  (Release) - 29 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha/Beta Barrel, Redox, Dehydrogenase, Fmn, Inhibitor, Mitochondrial Membrane, Oxidoreductase-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Phillips, J. Lotharius, K. Marsh, J. White, A. Dayan, K. L. White, J. W. Njoroge, F. El Mazouni, Y. Lao, S. Kokkonda, D. R. Tomchick, X. Deng, T. Laird, S. N. Bhatia, S. March, C. L. Ng, D. A. Fidock, S. Wittlin, M. Lafuente-Monasterio, F. J. Benito, L. M. Alonso, M. S. Martinez, M. B. Jimenez-Diaz, S. F. Bazaga, I. Angulo-Barturen, J. N. Haselden, J. Louttit, Y. Cui, A. Sridhar, A. M. Zeeman, C. Kocken, R. Sauerwein, K. Dechering, V. M. Avery, S. Duffy, M. Delves, R. Sinden A. Ruecker, K. S. Wickham, R. Rochford, J. Gahagen, L. Iyer, E. Riccio, J. Mirsalis, I. Bathhurst, T. Rueckle, X. Ding, B. Campo, D. Leroy, M. J. Rogers, P. K. Rathod, J. N. Burrows, S. A. Charman
A Long-Duration Dihydroorotate Dehydrogenase Inhibitor (Dsm265) For Prevention And Treatment Of Malaria.
Sci Transl Med V. 7 Ra111 2015
PubMed-ID: 26180101  |  Reference-DOI: 10.1126/SCITRANSLMED.AAA6645

(-) Compounds

Molecule 1 - DIHYDROOROTATE DEHYDROGENASE (QUINONE), MITOCHONDRIAL
    Chains: A, B
    EC Number: 1.3.5.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 158-569
    Gene: PFF0160C
    Organism Scientific: PLASMODIUM FALCIPARUM (ISOLATE 3D7)
    Organism Taxid: 36329
    Strain: ISOLATE 3D7
    Synonym: DHODEHASE,DIHYDROOROTATE OXIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1D652Ligand/Ion2-(1,1-DIFLUOROETHYL)-5-METHYL-N-[4-(PENTAFLUORO-LAMBDA~6~-SULFANYL)PHENYL][1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7-AMINE
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
3ORO2Ligand/IonOROTIC ACID
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1D651Ligand/Ion2-(1,1-DIFLUOROETHYL)-5-METHYL-N-[4-(PENTAFLUORO-LAMBDA~6~-SULFANYL)PHENYL][1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7-AMINE
2FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
3ORO1Ligand/IonOROTIC ACID
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1D651Ligand/Ion2-(1,1-DIFLUOROETHYL)-5-METHYL-N-[4-(PENTAFLUORO-LAMBDA~6~-SULFANYL)PHENYL][1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7-AMINE
2FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
3ORO1Ligand/IonOROTIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:172 , GLY A:181 , GLU A:182 , CYS A:184 , HIS A:185 , PHE A:188 , LEU A:197 , PHE A:227 , LEU A:240 , ILE A:263 , ARG A:265 , ILE A:272 , LEU A:531 , VAL A:532 , MET A:536binding site for residue D65 A 1001
2AC2SOFTWAREALA A:224 , ALA A:225 , GLY A:226 , LYS A:229 , THR A:249 , ASN A:274 , LYS A:429 , SER A:457 , ASN A:458 , SER A:477 , GLY A:478 , SER A:505 , GLY A:506 , GLY A:507 , TYR A:528 , SER A:529 , ORO A:1003binding site for residue FMN A 1002
3AC3SOFTWARELYS A:229 , ASN A:274 , CYS A:276 , GLY A:277 , PHE A:278 , ASN A:342 , SER A:344 , SER A:345 , ASN A:347 , ASN A:458 , THR A:459 , FMN A:1002binding site for residue ORO A 1003
4AC4SOFTWARELEU B:172 , GLY B:181 , GLU B:182 , CYS B:184 , HIS B:185 , PHE B:188 , LEU B:197 , PHE B:227 , LEU B:240 , ILE B:263 , ARG B:265 , ILE B:272 , LEU B:531 , MET B:536binding site for residue D65 B 1001
5AC5SOFTWAREALA B:224 , ALA B:225 , GLY B:226 , LYS B:229 , THR B:249 , ASN B:274 , LYS B:429 , SER B:457 , ASN B:458 , SER B:477 , GLY B:478 , SER B:505 , GLY B:506 , GLY B:507 , TYR B:528 , SER B:529 , ORO B:1003binding site for residue FMN B 1002
6AC6SOFTWARELYS B:229 , ASN B:274 , CYS B:276 , GLY B:277 , PHE B:278 , ASN B:342 , SER B:345 , ASN B:347 , ASN B:458 , THR B:459 , FMN B:1002binding site for residue ORO B 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5BOO)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Gly A:248 -Thr A:249
2Lys A:260 -Pro A:261
3Ile A:456 -Ser A:457
4Gly B:248 -Thr B:249
5Lys B:260 -Pro B:261
6Ile B:456 -Ser B:457

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5BOO)

(-) Sequences/Alignments

Asymmetric 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:374
                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhheee..eee...eee.........hhhhhhh....eeeeeee............eeee....eeee.......hhhhhhhhhhhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhh................eeeeee....hhhhhhhhhhhhhhh...eeee.........hhhhh....eeee..hhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhheeeeeehhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5boo A 162 NPEFFLYDIFLKFCLKYIDGEICHDLFLLLGKYNILPYDTSNDSIYACTNIKHLDFINPFGVAAGFDKNGVCIDSILKLGFSFIEIGTITPRGQTGNAKPRIFRDVESRSIINSCGFNNMGCDKVTENLILFRKRQEEDKLLSKHIVGVSIGKNKDTVNIVDDLKYCINKIGRYADYIAINVSSPNTPGLRDNQEAGKLKNIILSVKEEIDNLEKNNIMNDEFLWFNTTKKKPLVFVKLAPDLNQEQKKEIADVLLETNIDGMIISNTTTQINDIKSFENKKGGVSGAKLKDISTKFICEMYNYTNKQIPIIASGGIFSGLDALEKIEAGASVCQLYSCLVFNGMKSAVQIKRELNHLLYQRGYYNLKEAIGRK 565
                                   171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381 ||    421       431       441       451       461       471       481       491       501       511       521       531       541       551       561    
                                                                                                                                                                                                                                                       383|                                                                                                                                                       
                                                                                                                                                                                                                                                        414                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:373
                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhheee..eee...eee.........hhhhhhh....eeeeeee............eeee....eeee.......hhhhhhhhhhhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhh................eeeeee....hhhhhhhhhhhhhhh...eeee.........hhhhh....eeee..hhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhheeeeeehhhhhhh..hhhhhhhhhhhhhhhhh....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5boo B 162 NPEFFLYDIFLKFCLKYIDGEICHDLFLLLGKYNILPYDTSNDSIYACTNIKHLDFINPFGVAAGFDKNGVCIDSILKLGFSFIEIGTITPRGQTGNAKPRIFRDVESRSIINSCGFNNMGCDKVTENLILFRKRQEEDKLLSKHIVGVSIGKNKDTVNIVDDLKYCINKIGRYADYIAINVSSPNTPGLRDNQEAGKLKNIILSVKEEIDNLEKNNIMNDEFLWFNTTKKKPLVFVKLAPDLNQEQKKEIADVLLETNIDGMIISNTTTQINDIKSFENKKGGVSGAKLKDISTKFICEMYNYTNKQIPIIASGGIFSGLDALEKIEAGASVCQLYSCLVFNGMKSAVQIKRELNHLLYQRGYYNLKEAIGR 564
                                   171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381 ||    421       431       441       451       461       471       481       491       501       511       521       531       541       551       561   
                                                                                                                                                                                                                                                       383|                                                                                                                                                      
                                                                                                                                                                                                                                                        414
   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 5BOO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    D65  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FMN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ORO  [ 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 ]
 
  Cis Peptide Bonds
    Gly A:248 - Thr A:249   [ RasMol ]  
    Gly B:248 - Thr B:249   [ RasMol ]  
    Ile A:456 - Ser A:457   [ RasMol ]  
    Ile B:456 - Ser B:457   [ RasMol ]  
    Lys A:260 - Pro A:261   [ RasMol ]  
    Lys B:260 - Pro B:261   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  5boo
    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
  PYRD_PLAF7 | Q08210
    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)
  1.3.5.2
    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
  PYRD_PLAF7 | Q08210
    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
        PYRD_PLAF7 | Q08210: 1tv5 3i65 3i68 3i6r 3o8a 3sfk 4cq8 4cq9 4cqa 4orm 4rx0 5del 5fi8 5tbo

(-) Related Entries Specified in the PDB File

4rx0 4RX0 WITH A DIFFERENT SPACE GROUP