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(-) Description

Title :  PHOSPHONIC ARGININE MIMETICS AS INHIBITORS OF THE M1 AMINOPEPTIDASES FROM PLASMODIUM FALCIPARUM
 
Authors :  S. Mcgowan
Date :  14 Apr 13  (Deposition) - 12 Jun 13  (Release) - 24 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  M1 Alanyl-Aminopeptidase, Protease, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Kannan Sivaraman, A. Paiardini, M. Sienczyk, C. Ruggeri, C. A. Oellig, J. P. Dalton, P. J. Scammells, M. Drag, S. Mcgowan
Synthesis And Structure-Activity Relationships Of Phosphoni Arginine Mimetics As Inhibitors Of The M1 And M17 Aminopeptidases From Plasmodium Falciparum.
J. Med. Chem. V. 56 5213 2013
PubMed-ID: 23713488  |  Reference-DOI: 10.1021/JM4005972

(-) Compounds

Molecule 1 - M1 FAMILY AMINOPEPTIDASE
    Chains: A
    EC Number: 3.4.11.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PTRC-HIS2B
    Fragment: UNP RESIDUES 195-1085
    Mutation: YES
    Organism Scientific: PLASMODIUM FALCIPARUM FCB1/COLUMBIA
    Organism Taxid: 186763
    Synonym: PFA-M1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
11OV1Ligand/Ion[(1R)-1-AMINO-4-CARBAMIMIDAMIDOBUTYL]PHOSPHONIC ACID
2GOL3Ligand/IonGLYCEROL
3MG2Ligand/IonMAGNESIUM ION
4ZN1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:496 , HIS A:500 , GLU A:519 , 1OV A:1106BINDING SITE FOR RESIDUE ZN A 1101
2AC2SOFTWAREGLY A:250 , HOH A:1340 , HOH A:2287 , HOH A:2288 , HOH A:2289 , HOH A:2290BINDING SITE FOR RESIDUE MG A 1102
3AC3SOFTWAREGLU A:957 , HOH A:1720 , HOH A:2051 , HOH A:2300 , HOH A:2301 , HOH A:2302BINDING SITE FOR RESIDUE MG A 1103
4AC4SOFTWARETYR A:765 , CYS A:768 , THR A:769 , TYR A:772 , TYR A:823 , SER A:826 , PRO A:828BINDING SITE FOR RESIDUE GOL A 1104
5AC5SOFTWARELYS A:479 , TYR A:880 , VAL A:887 , ASP A:888 , GLN A:891 , ARG A:895 , TYR A:925 , HOH A:2269BINDING SITE FOR RESIDUE GOL A 1105
6AC6SOFTWAREGLU A:319 , PHE A:457 , ASN A:458 , VAL A:459 , ALA A:461 , GLU A:463 , HIS A:496 , GLU A:497 , HIS A:500 , LYS A:518 , GLU A:519 , TYR A:575 , TYR A:580 , ZN A:1101 , GOL A:1107 , HOH A:1542 , HOH A:2193 , HOH A:2274BINDING SITE FOR RESIDUE 1OV A 1106
7AC7SOFTWAREVAL A:493 , HIS A:496 , GLU A:526 , TYR A:580 , 1OV A:1106 , HOH A:1532 , HOH A:1542 , HOH A:2022 , HOH A:2193BINDING SITE FOR RESIDUE GOL A 1107

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K5M)

(-) 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 4K5M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K5M)

(-) Exons   (0, 0)

(no "Exon" information available for 4K5M)

(-) 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
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.hhh....eeeeeeeeeeee....eeeeeeeeeee........eeee....eeeeeee..ee......eee...eeee.hhhh....eeeeeeeeehhhhh....eeeee..eeeee....hhhhh..........eeeeeeeeee.....eeee..eeeeeeee...eeeeeeeeeeeehhhhh.eeee.eeeeeeeee......eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee......ee....eeeee.hhh........hhhhhhhhhhhhhhhhh.......ee.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.........ee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhh......hhhhhhhhh....eeeeeeeee....eeeeeeeee..............eeeeeeee...........eeeee...eeeeee.......eeee........eee...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh....hhhhhhhhh...hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4k5m 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)
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  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 4K5M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K5M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K5M)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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    Glu A:319 - Ala A:320   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        AMP1_PLAFQ | O96935: 3ebg 3ebh 3ebi 3q43 3q44 3t8v 4j3b 4k5l 4k5n 4k5o 4k5p 4r5t 4r5v 4r5x 4x2u 4zqt 4zw3 4zw5 4zw6 4zw7 4zw8 4zx3 4zx4 4zx5 4zx6

(-) Related Entries Specified in the PDB File

4k3n 4k5l 4k5n 4k5o 4k5p