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(-) Description

Title :  STRUCTURE OF THE M1 ALANYLAMINOPEPTIDASE FROM MALARIA COMPLEXED WITH A HYDROXAMIC ACID-BASED INHIBITOR
 
Authors :  N. Drinkwater, S. Mcgowan
Date :  22 Aug 14  (Deposition) - 29 Oct 14  (Release) - 26 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Protease, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. N. Mistry, N. Drinkwater, C. Ruggeri, K. K. Sivaraman, S. Loganathan, S. Fletcher, M. Drag, A. Paiardini, V. M. Avery, P. J. Scammells, S. Mcgowan
Two-Pronged Attack: Dual Inhibition Of Plasmodium Falciparu M1 And M17 Metalloaminopeptidases By A Novel Series Of Hydroxamic Acid-Based Inhibitors.
J. Med. Chem. V. 57 9168 2014
PubMed-ID: 25299353  |  Reference-DOI: 10.1021/JM501323A

(-) Compounds

Molecule 1 - M1 FAMILY AMINOPEPTIDASE
    Chains: A
    EC Number: 3.4.11.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRCHIS-2B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 195-1084
    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  (5, 12)

Asymmetric/Biological Unit (5, 12)
No.NameCountTypeFull Name
1DMS5Ligand/IonDIMETHYL SULFOXIDE
2GOL4Ligand/IonGLYCEROL
3MG1Ligand/IonMAGNESIUM ION
4R5X1Ligand/Ion3-AMINO-N-{(1R)-2-(HYDROXYAMINO)-2-OXO-1-[4-(1H-PYRAZOL-1-YL)PHENYL]ETHYL}BENZAMIDE
5ZN1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:496 , HIS A:500 , GLU A:519 , R5X A:1107BINDING SITE FOR RESIDUE ZN A 1101
02AC2SOFTWAREVAL A:459 , ASN A:471 , ASN A:473 , SER A:474 , ARG A:489 , ARG A:997 , HOH A:1201 , HOH A:1692BINDING SITE FOR RESIDUE GOL A 1102
03AC3SOFTWAREMET A:533 , THR A:534 , VAL A:887 , ASP A:888 , PHE A:889 , ASP A:890 , DMS A:1112 , HOH A:1560 , HOH A:1947BINDING SITE FOR RESIDUE GOL A 1103
04AC4SOFTWARETYR A:575 , THR A:576 , THR A:577 , TYR A:580 , ASP A:581 , R5X A:1107BINDING SITE FOR RESIDUE GOL A 1104
05AC5SOFTWAREGLY A:250 , HOH A:1357 , HOH A:1400 , HOH A:1483 , HOH A:1484 , HOH A:2034BINDING SITE FOR RESIDUE MG A 1105
06AC6SOFTWARELYS A:479 , TYR A:880 , VAL A:887 , ASP A:888 , GLN A:891 , ARG A:895 , TYR A:925 , HOH A:1210 , HOH A:1280BINDING SITE FOR RESIDUE GOL A 1106
07AC7SOFTWAREGLU A:319 , VAL A:459 , GLY A:460 , ALA A:461 , MET A:462 , GLU A:463 , ARG A:489 , HIS A:496 , GLU A:497 , HIS A:500 , GLU A:519 , TYR A:575 , TYR A:580 , MET A:1034 , ZN A:1101 , GOL A:1104 , HOH A:1601 , HOH A:1692 , HOH A:1775 , HOH A:2029 , HOH A:2032BINDING SITE FOR RESIDUE R5X A 1107
08AC8SOFTWAREASN A:573 , THR A:1037 , TYR A:1077 , HOH A:1335BINDING SITE FOR RESIDUE DMS A 1108
09AC9SOFTWARETYR A:853 , SER A:903 , LYS A:907 , DMS A:1110 , HOH A:1315 , HOH A:1362BINDING SITE FOR RESIDUE DMS A 1109
10BC1SOFTWAREVAL A:825 , SER A:826 , TYR A:853 , SER A:903 , DMS A:1109BINDING SITE FOR RESIDUE DMS A 1110
11BC2SOFTWAREVAL A:245 , ASP A:247 , PHE A:275 , HOH A:1766BINDING SITE FOR RESIDUE DMS A 1111
12BC3SOFTWAREHIS A:886 , VAL A:887 , ASP A:888 , GOL A:1103BINDING SITE FOR RESIDUE DMS A 1112

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R5X)

(-) 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 4R5X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R5X)

(-) Exons   (0, 0)

(no "Exon" information available for 4R5X)

(-) 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:888
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               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.hhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee......ee....eeeee.hhh........hhhhhhhhhhhhhhhhhhhhhh.eee.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.........ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh......hhhhhhhhh....eeeeeeeee....eeeeeeeee..............eeeeeeee...........eeeee...eeeeee.......eeee........eee...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh....hhhhhhhhh...hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4r5x A  197 KIHYRKDYKPSGFIINQVTLNINIHDQETIVRSVLDMDISKHNVGEDLVFDGVGLKINEISINNKKLVEGEEYTYDNEFLTIFSKFVPKSKFAFSSEVIIHPETNYALTGLYKSKNIIVSQCEATGFRRITFFIDRPDMMAKYDVTVTADKEKYPVLLSNGDKVNEFEIPGGRHGARFNDPPLKPCYLFAVVAGDLKHLSATYITKYTKKKVELYVFSEEKYVSKLQWALECLKKSMAFDEDYFGLEYDLSRLNLVAVSDFNVGAMENKGLNIFNANSLLASKKNSIDFSYARILTVVGHEYFHQYTGNRVTLRDWFQLTLKEGLTVHRENLFSEEMTKTVTTRLSHVDLLRSVQFLEDSSPLSHPIRPESYVSMENFYTTTVYDKGSEVMRMYLTILGEEYYKKGFDIYIKKNDGNTATCEDFNYAMEQAYKMKKADNSANLNQYLLWFSQSGTPHVSFKYNYDAEKKQYSIHVNQYTKPDENQKEKKPLFIPISVGLINPENGKEMISQTTLELTKESDTFVFNNIAVKPIPSLFRGFSAPVYIEDQLTDEERILLLKYDSDAFVRYNSCTNIYMKQILMNYNEFLKAKNEKLESFQLTPVNAQFIDAIKYLLEDPHADAGFKSYIVSLPQDRYIINFVSNLDTDVLADTKEYIYKQIGDKLNDVYYKMFKSLEAKADDLTYFNDESHVDFDQMNMRTLRNTLLSLLSKAQYPNILNEIIEHSKSPYPSNWLTSLSVSAYFDKYFELYDKTYKLSKDDELLLQEWLKTVSRSDRKDIYEILKKLENEVLKDSKNPNDIRAVYLPFTNNLRRFHDISGKGYKLIAEVITKTDKFNPMVATQLCEPFKLWNKLDTKRQELMLNEMNTMLQEPQISNNLKEYLLRLTNK 1084
                                   206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896       906       916       926       936       946       956       966       976       986       996      1006      1016      1026      1036      1046      1056      1066      1076
   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 4R5X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R5X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R5X)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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  3.4.11.-
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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 4k5m 4k5n 4k5o 4k5p 4r5t 4r5v 4x2u 4zqt 4zw3 4zw5 4zw6 4zw7 4zw8 4zx3 4zx4 4zx5 4zx6

(-) Related Entries Specified in the PDB File

3ebg UNLIGANDED FORM OF ENZYME
4r5t
4r5v
4r6t
4r76
4r7m