Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
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 :  X-RAY CRYSTAL STRUCTURE OF THE ASPARTIC PROTEASE PLASMEPSIN 4 FROM THE MALARIAL PARASITE PLASMODIUM MALARIAE BOUND TO AN ALLOPHENYLNORSTATINE BASED INHIBITOR
 
Authors :  J. C. Clemente, L. Govindasamy, A. Madabushi, S. Z. Fisher, R. E. Moose, C. A. Yowell, K. Hidaka, T. Kimura, Y. Hayashi, Y. Kiso, M. Agbandje-Mc J. B. Dame, B. M. Dunn, R. Mckenna
Date :  11 Aug 05  (Deposition) - 04 Apr 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Plasmodium Parasite, Plasmepsin 4, Aspartic Protease, Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. C. Clemente, L. Govindasamy, A. Madabushi, S. Z. Fisher, R. E. Moose C. A. Yowell, K. Hidaka, T. Kimura, Y. Hayashi, Y. Kiso, M. Agbandje-Mckenna, J. B. Dame, B. M. Dunn, R. Mckenna
Structure Of The Aspartic Protease Plasmepsin 4 From The Malarial Parasite Plasmodium Malariae Bound To An Allophenylnorstatine-Based Inhibitor.
Acta Crystallogr. , Sect. D V. 62 246 2006
PubMed-ID: 16510971  |  Reference-DOI: 10.1107/S0907444905041260

(-) Compounds

Molecule 1 - PLASMEPSIN IV
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: PLASMODIUM MALARIAE
    Organism Taxid: 5858

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1JE22Ligand/Ion(4R)-3-{(2S,3S)-2-HYDROXY-3-[(3-HYDROXY-2-METHYLBENZOYL)AMINO]-4-PHENYLBUTANOYL}-5,5-DIMETHYL-N-(2-METHYLBENZYL)-1,3-THIAZOLIDINE-4-CARBOXAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1JE21Ligand/Ion(4R)-3-{(2S,3S)-2-HYDROXY-3-[(3-HYDROXY-2-METHYLBENZOYL)AMINO]-4-PHENYLBUTANOYL}-5,5-DIMETHYL-N-(2-METHYLBENZYL)-1,3-THIAZOLIDINE-4-CARBOXAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1JE21Ligand/Ion(4R)-3-{(2S,3S)-2-HYDROXY-3-[(3-HYDROXY-2-METHYLBENZOYL)AMINO]-4-PHENYLBUTANOYL}-5,5-DIMETHYL-N-(2-METHYLBENZYL)-1,3-THIAZOLIDINE-4-CARBOXAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:34 , GLY A:36 , TYR A:77 , GLY A:78 , SER A:79 , LEU A:131 , PHE A:192 , ASP A:214 , THR A:217 , VAL A:292 , HOH A:402BINDING SITE FOR RESIDUE JE2 A 3151
2AC2SOFTWAREASP B:34 , GLY B:36 , TYR B:77 , GLY B:78 , SER B:79 , LEU B:131 , PHE B:192 , ASP B:214 , THR B:217 , VAL B:292 , HOH B:409BINDING SITE FOR RESIDUE JE2 B 3152

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:47 -A:52
2A:249 -A:285
3B:47 -B:52
4B:249 -B:285

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ANL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ANL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ANL)

(-) Exons   (0, 0)

(no "Exon" information available for 2ANL)

(-) 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:327
 aligned with O60990_PLAMA | O60990 from UniProtKB/TrEMBL  Length:451

    Alignment length:327
                                   134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       
         O60990_PLAMA   125 SENDVIELDDVANLMFYGEGEVGDNHQKFMLIFDTGSANLWVPSKKCNSIGCSTKHLYDSSKSKSYEKDGTKVEITYGSGTVRGFFSKDLVTLGYLSLPYKFIEVTDTDDLEPLYTAAEFDGILGLGWKDLSIGSIDPIVVELKNQNKIDQALFTFYLPVHDKHSGYLTIGGIEEKFYEGELTYEKLNHDLFWQVDLDVNFGKTSMEKANVIVDSGTSTITAPTSFINKFFKDLNVIKVPFLPFYITTCNNKDMPTLEFKSANNTYTLEPEYYMEPLLDIDDTLCMLYILPVDIDKNTFILGDPFMRKYFTVFDYDKESIGFAVAKN 451
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2anlA01 A:1-175 Acid Proteases                                                                                                                                                 2anlA02 A:176-327 Acid Proteases                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee...eeeeeeee....eeee..ee.....eeee.....hhhhhh.................eeee......eeeeeeeeeee......eeeeeeeee.....hhhhhh....eee..hhhhh.......hhhhhh.......eeeee........eeeee...hhh.eeeeeeeee.......eeeeeeee..eeeeeeeeee......eeehhhhhhhhhhhh..ee......eeee........eeee....eeeehhhh.eee.......eeee.eee......eeeehhhhhhheeeeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2anl A   1 SENDVIELDDVANLMFYGEGEVGDNHQKFMLIFDTGSANLWVPSKKCNSIGCSTKHLYDSSKSKSYEKDGTKVEITYGSGTVRGFFSKDLVTLGYLSLPYKFIEVTDTDDLEPLYTAAEFDGILGLGWKDLSIGSIDPIVVELKNQNKIDQALFTFYLPVHDKHSGYLTIGGIEEKFYEGELTYEKLNHDLFWQVDLDVNFGKTSMEKANVIVDSGTSTITAPTSFINKFFKDLNVIKVPFLPFYITTCNNKDMPTLEFKSANNTYTLEPEYYMEPLLDIDDTLCMLYILPVDIDKNTFILGDPFMRKYFTVFDYDKESIGFAVAKN 327
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       


Chain B from PDB  Type:PROTEIN  Length:327
 aligned with O60990_PLAMA | O60990 from UniProtKB/TrEMBL  Length:451

    Alignment length:327
                                   134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       
         O60990_PLAMA   125 SENDVIELDDVANLMFYGEGEVGDNHQKFMLIFDTGSANLWVPSKKCNSIGCSTKHLYDSSKSKSYEKDGTKVEITYGSGTVRGFFSKDLVTLGYLSLPYKFIEVTDTDDLEPLYTAAEFDGILGLGWKDLSIGSIDPIVVELKNQNKIDQALFTFYLPVHDKHSGYLTIGGIEEKFYEGELTYEKLNHDLFWQVDLDVNFGKTSMEKANVIVDSGTSTITAPTSFINKFFKDLNVIKVPFLPFYITTCNNKDMPTLEFKSANNTYTLEPEYYMEPLLDIDDTLCMLYILPVDIDKNTFILGDPFMRKYFTVFDYDKESIGFAVAKN 451
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2anlB01 B:1-175 Acid Proteases                                                                                                                                                 2anlB02 B:176-327 Acid Proteases                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee...eeeeeeee....eeee..ee.....eeee.....hhhhhh.................eeee......eeeeeeeeeee......eeeeeeeee.....hhhhhh....eee..hhhhh.......hhhhhh.......eeeee........eeeee...hhh.eeeeeeeee.......eeeeeeee..eeeeeeeeee......eeehhhhhhhhhhhh..ee......eeee........eeee....eeeehhhh.eee.......eeee.eee......eeeehhhhhhheeeeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2anl B   1 SENDVIELDDVANLMFYGEGEVGDNHQKFMLIFDTGSANLWVPSKKCNSIGCSTKHLYDSSKSKSYEKDGTKVEITYGSGTVRGFFSKDLVTLGYLSLPYKFIEVTDTDDLEPLYTAAEFDGILGLGWKDLSIGSIDPIVVELKNQNKIDQALFTFYLPVHDKHSGYLTIGGIEEKFYEGELTYEKLNHDLFWQVDLDVNFGKTSMEKANVIVDSGTSTITAPTSFINKFFKDLNVIKVPFLPFYITTCNNKDMPTLEFKSANNTYTLEPEYYMEPLLDIDDTLCMLYILPVDIDKNTFILGDPFMRKYFTVFDYDKESIGFAVAKN 327
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320
   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 2ANL)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2ANL)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (O60990_PLAMA | O60990)
molecular function
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 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
    JE2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2anl)
 
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
  2anl
    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
  O60990_PLAMA | O60990
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  O60990_PLAMA | O60990
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2ANL)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2ANL)