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(-) Description

Title :  STRUCTURE OF THE M1 ALANYLAMINOPEPTIDASE FROM MALARIA COMPLEXED WITH THE PHOSPHINATE DIPEPTIDE ANALOG
 
Authors :  S. Mcgowan, C. J. Porter, A. M. Buckle, J. C. Whisstock
Date :  27 Aug 08  (Deposition) - 27 Jan 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Aminopeptidase, Metal-Binding, Metalloprotease, Protease, Hydrolase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Mcgowan, C. J. Porter, J. Lowther, C. M. Stack, S. J. Golding, T. S. Skinner-Adams, K. R. Trenholme, F. Teuscher, S. M. Donnelly, J. Grembecka, A. Mucha, P. Kafarski, R. Degori, A. M. Buckle, D. L. Gardiner, J. C. Whisstock, J. P. Dalton
Structural Basis For The Inhibition Of The Essential Plasmodium Falciparum M1 Neutral Aminopeptidase
Proc. Natl. Acad. Sci. Usa V. 106 2537 2009
PubMed-ID: 19196988  |  Reference-DOI: 10.1073/PNAS.0807398106

(-) Compounds

Molecule 1 - M1 FAMILY AMINOPEPTIDASE
    ChainsA
    EC Number3.4.11.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTRCHIS2B
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 195 TO 1084
    Organism ScientificPLASMODIUM FALCIPARUM
    Organism Taxid186763
    StrainD10
    SynonymPFA-M1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1BEY1Ligand/Ion(2S)-3-[(R)-[(1S)-1-AMINO-3-PHENYLPROPYL](HYDROXY)PHOSPHORYL]-2-BENZYLPROPANOIC ACID
2GOL5Ligand/IonGLYCEROL
3MG4Ligand/IonMAGNESIUM ION
4ZN1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:496 , HIS A:500 , GLU A:519 , BEY A:1085BINDING SITE FOR RESIDUE ZN A 1
02AC2SOFTWAREZN A:1 , GLN A:317 , GLU A:319 , VAL A:459 , GLY A:460 , ALA A:461 , MET A:462 , GLU A:463 , ARG A:489 , VAL A:493 , HIS A:496 , GLU A:497 , HIS A:500 , GLU A:519 , TYR A:575 , TYR A:580 , MET A:1034 , HOH A:1544 , HOH A:1545BINDING SITE FOR RESIDUE BEY A1085
03AC3SOFTWAREHOH A:19 , LYS A:479 , TYR A:880 , HIS A:886 , VAL A:887 , ASP A:888 , GLN A:891 , MET A:892 , ARG A:895 , TYR A:925 , HOH A:1513BINDING SITE FOR RESIDUE GOL A1086
04AC4SOFTWAREHOH A:100 , HOH A:103 , HOH A:1473 , HOH A:1542 , HOH A:1543BINDING SITE FOR RESIDUE MG A 10
05AC5SOFTWARETYR A:765 , CYS A:768 , THR A:769 , TYR A:772 , TYR A:823 , SER A:826 , PRO A:828 , HOH A:1502BINDING SITE FOR RESIDUE GOL A 2
06AC6SOFTWAREHOH A:105 , HIS A:653 , LYS A:676 , TYR A:741 , ASN A:835 , HOH A:1417BINDING SITE FOR RESIDUE GOL A 3
07AC7SOFTWAREHOH A:62 , VAL A:459 , GLY A:460 , ASN A:471 , ASN A:473 , SER A:474 , ARG A:489 , ARG A:997BINDING SITE FOR RESIDUE GOL A 4
08AC8SOFTWAREILE A:483 , LEU A:930 , THR A:931 , SER A:934 , THR A:966 , ARG A:969 , HOH A:1116 , HOH A:1154 , HOH A:1369BINDING SITE FOR RESIDUE GOL A 5
09AC9SOFTWAREHOH A:26 , GLY A:250 , HOH A:1099 , HOH A:1214 , HOH A:1536BINDING SITE FOR RESIDUE MG A 7
10BC1SOFTWAREHOH A:1177 , HOH A:1537 , HOH A:1538 , HOH A:1539 , HOH A:1540BINDING SITE FOR RESIDUE MG A 8
11BC2SOFTWAREGLU A:957 , HOH A:1541BINDING SITE FOR RESIDUE MG A 9

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EBI)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:319 -Ala A:320

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EBI)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.AMP1_PLAFQ493-502  1A:493-502

(-) Exons   (0, 0)

(no "Exon" information available for 3EBI)

(-) 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:889
 aligned with AMP1_PLAFQ | O96935 from UniProtKB/Swiss-Prot  Length:1085

    Alignment length:889
                                   205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025      1035      1045      1055      1065      1075         
          AMP1_PLAFQ    196 PKIHYRKDYKPSGFIINNVTLNINIHDNETIVRSVLDMDISKHNVGEDLVFDGVGLKINEISINNKKLVEGEEYTYDNEFLTIFSKFVPKSKFAFSSEVIIHPETNYALTGLYKSKNIIVSQCEATGFRRITFFIDRPDMMAKYDVTVTADKEKYPVLLSNGDKVNEFEIPGGRHGARFNDPHLKPCYLFAVVAGDLKHLSATYITKYTKKKVELYVFSEEKYVSKLQWALECLKKSMAFDEDYFGLEYDLSRLNLVAVSDFNVGAMENKGLNIFNANSLLASKKNSIDFSYARILTVVGHEYFHNYTGNRVTLRDWFQLTLKEGLTVHRENLFSEEMTKTVTTRLSHVDLLRSVQFLEDSSPLSHPIRPESYVSMENFYTTTVYDKGSEVMRMYLTILGEEYYKKGFDIYIKKNDGNTATCEDFNYAMEQAYKMKKADNSANLNQYLLWFSQSGTPHVSFKYNYDAEKKQYSIHVNQYTKPDENQKEKKPLFIPISVGLINPENGKEMISQTTLELTKESDTFVFNNIAVKPIPSLFRGFSAPVYIEDNLTDEERILLLKYDSDAFVRYNSCTNIYMKQILMNYNEFLKAKNEKLESFNLTPVNAQFIDAIKYLLEDPHADAGFKSYIVSLPQDRYIINFVSNLDTDVLADTKEYIYKQIGDKLNDVYYKMFKSLEAKADDLTYFNDESHVDFDQMNMRTLRNTLLSLLSKAQYPNILNEIIEHSKSPYPSNWLTSLSVSAYFDKYFELYDKTYKLSKDDELLLQEWLKTVSRSDRKDIYEILKKLENEVLKDSKNPNDIRAVYLPFTNNLRRFHDISGKGYKLIAEVITKTDKFNPMVATQLCEPFKLWNKLDTKRQELMLNEMNTMLQEPNISNNLKEYLLRLTNK 1084
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeeeeeeee....eeeeeeeeeee........eeee....eeeeeee..........eee...eeee.........eeeeeeeee.........eeeee..eeeee...................eeeeeeeeee.....eeee..eeeeeeee...eeeeeeeeeeee......eeee.eeeeeeeee......eeeeeeeee......hhhhhhhhhhhhhhhhhhh.......eeeeeee............eeeee............hhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...................eeeeeeeeee....eeeeeeeeee.............eeeeeeeee..........eeeee...eeeeee.......eee.........eee....hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh.....hhhhhhhh....hhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh....hhhhhhhhh....hhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhh......hhhhhhhhh.....hhhhh....hhhhhhhhhhhhhhh..hhhhhhhh..........hhhhhhhhhhhhhhhh.....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ebi A  196 PKIHYRKDYKPSGFIINQVTLNINIHDQETIVRSVLDMDISKHNVGEDLVFDGVGLKINEISINNKKLVEGEEYTYDNEFLTIFSKFVPKSKFAFSSEVIIHPETNYALTGLYKSKNIIVSQCEATGFRRITFFIDRPDMMAKYDVTVTADKEKYPVLLSNGDKVNEFEIPGGRHGARFNDPPLKPCYLFAVVAGDLKHLSATYITKYTKKKVELYVFSEEKYVSKLQWALECLKKSMAFDEDYFGLEYDLSRLNLVAVSDFNVGAMENKGLNIFNANSLLASKKNSIDFSYARILTVVGHEYFHQYTGNRVTLRDWFQLTLKEGLTVHRENLFSEEMTKTVTTRLSHVDLLRSVQFLEDSSPLSHPIRPESYVSMENFYTTTVYDKGSEVMRMYLTILGEEYYKKGFDIYIKKNDGNTATCEDFNYAMEQAYKMKKADNSANLNQYLLWFSQSGTPHVSFKYNYDAEKKQYSIHVNQYTKPDENQKEKKPLFIPISVGLINPENGKEMISQTTLELTKESDTFVFNNIAVKPIPSLFRGFSAPVYIEDQLTDEERILLLKYDSDAFVRYNSCTNIYMKQILMNYNEFLKAKNEKLESFQLTPVNAQFIDAIKYLLEDPHADAGFKSYIVSLPQDRYIINFVSNLDTDVLADTKEYIYKQIGDKLNDVYYKMFKSLEAKADDLTYFNDESHVDFDQMNMRTLRNTLLSLLSKAQYPNILNEIIEHSKSPYPSNWLTSLSVSAYFDKYFELYDKTYKLSKDDELLLQEWLKTVSRSDRKDIYEILKKLENEVLKDSKNPNDIRAVYLPFTNNLRRFHDISGKGYKLIAEVITKTDKFNPMVATQLCEPFKLWNKLDTKRQELMLNEMNTMLQEPQISNNLKEYLLRLTNK 1084
                                   205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025      1035      1045      1055      1065      1075         

   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 3EBI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3EBI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EBI)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AMP1_PLAFQ | O96935)
molecular function
    GO:0004177    aminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AMP1_PLAFQ | O969353ebg 3ebh 3q43 3q44 3t8v 4j3b 4k5l 4k5m 4k5n 4k5o 4k5p 4r5t 4r5v 4r5x 4x2u 4zqt 4zw3 4zw5 4zw6 4zw7 4zw8 4zx3 4zx4 4zx5 4zx6

(-) Related Entries Specified in the PDB File

3ebg 3ebh