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

(-) Description

Title :  LEISHMANIA MAJOR N-MYRISTOYLTRANSFERASE IN COMPLEX WITH AN AMINOACYLPYRROLIDINE INHIBITOR (2B)
 
Authors :  J. A. Hutton, V. Goncalves, J. A. Brannigan, D. Paape, T. Waugh, S. M. Rob A. S. Bell, A. J. Wilkinson, D. F. Smith, R. J. Leatherbarrow, E. W. Tate
Date :  14 Apr 14  (Deposition) - 01 Oct 14  (Release) - 05 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Myristoylation, Inhibitor, Drug Design (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Hutton, V. Goncalves, J. A. Brannigan, D. Paape, M. H. Wright, T. M. Waugh, S. M. Roberts, A. S. Bell, A. J. Wilkinson, D. F. Smith, R. J. Leatherbarrow, E. W. Tate
Structure-Based Design Of Potent And Selective Leishmania N- Myristoyltransferase Inhibitors.
J. Med. Chem. V. 57 8664 2014
PubMed-ID: 25238611  |  Reference-DOI: 10.1021/JM5011397

(-) Compounds

Molecule 1 - GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE
    Chains: A
    EC Number: 2.3.1.97
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MAC040-B01
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA2 PLYSS
    Expression System Vector: PET15
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 11-421
    Organism Scientific: LEISHMANIA MAJOR
    Organism Taxid: 5664

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1A6M1Ligand/Ion(3R)-3-AMINO-4-(4-CHLOROPHENYL)-1-[(3R,4S)-3-(4-CHLOROPHENYL)-4-(HYDROXYMETHYL)PYRROLIDIN-1-YL]BUTAN-1-ONE
2MG1Ligand/IonMAGNESIUM ION
3MYA1Ligand/IonTETRADECANOYL-COA

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:175 , GLU A:177 , LYS A:178 , ARG A:179 , LEU A:180 , MYA A:1001BINDING SITE FOR RESIDUE MG A 999
2AC2SOFTWARETYR A:80 , PHE A:90 , ASN A:167 , THR A:203 , TYR A:217 , PHE A:218 , HIS A:219 , TYR A:326 , ILE A:328 , TYR A:345 , ASN A:376 , MET A:377 , LEU A:399 , MET A:420 , LEU A:421 , MYA A:1001 , HOH A:2299BINDING SITE FOR RESIDUE A6M A1000
3AC3SOFTWAREHIS A:12 , ALA A:13 , PHE A:14 , TRP A:15 , ASN A:79 , TYR A:80 , VAL A:81 , PHE A:168 , LEU A:169 , CYS A:170 , VAL A:171 , ARG A:176 , GLU A:177 , LYS A:178 , ARG A:179 , LEU A:180 , ALA A:181 , PRO A:182 , THR A:189 , VAL A:192 , TRP A:198 , TYR A:202 , THR A:203 , LEU A:208 , TYR A:404 , MG A:999 , A6M A:1000 , HOH A:2001 , HOH A:2312 , HOH A:2318 , HOH A:2549 , HOH A:2550 , HOH A:2551 , HOH A:2552 , HOH A:2553 , HOH A:2554 , HOH A:2555BINDING SITE FOR RESIDUE MYA A1001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:209 -Thr A:210

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CYN)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4CYN)

(-) 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:411
 aligned with Q4Q5S8_LEIMA | Q4Q5S8 from UniProtKB/TrEMBL  Length:421

    Alignment length:411
                                    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       330       340       350       360       370       380       390       400       410       420 
         Q4Q5S8_LEIMA    11 AHAFWSTQPVPQTEDETEKIVFAGPMDEPKTVADIPEEPYPIASTFEWWTPNMEAADDIHAIYELLRDNYVEDDDSMFRFNYSEEFLQWALCPPNYIPDWHVAVRRKADKKLLAFIAGVPVTLRMGTPKYMKVKAQEKGEGEEAAKYDEPRHICEINFLCVHKQLREKRLAPILIKEATRRVNRTNVWQAVYTAGVLLPTPYASGQYFHRSLNPEKLVEIRFSGIPAQYQKFQNPMAMLKRNYQLPSAPKNSGLREMKPSDVPQVRRILMNYLDSFDVGPVFSDAEISHYLLPRDGVVFTYVVENDKKVTDFFSFYRIPSTVIGNSNYNLLNAAYVHYYAATSIPLHQLILDLLIVAHSRGFDVCNMVEILDNRSFVEQLKFGAGDGHLRYYFYNWAYPKIKPSQVALVML 421
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh....hhhhhhh...........hhhhh..........eeee.....hhhhhhhhhhhhhhhh.......eee..hhhhhhhhhh....hhh.eeeeee.....eeeeeeeeeeeee...hhhhhhhhhhh.hhhhhhh....eeeeeeeeeee.hhhh..hhhhhhhhhhhhhhhh.....eeeee........eeeeeeeee.hhhhhhhh.....hhhhhhh.hhhhhhhhhhh.........eee.hhhhhhhhhhhhhhhhh....ee..hhhhhhhhhh.....eeeeeeee..eeeeeeeeeeeeeee.......eeeeeeeeeeee...hhhhhhhhhhhhhhhh...eeeee...hhhhhh.....eeeeeeeeeeee.......hhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cyn A  11 AHAFWSTQPVPQTEDETEKIVFAGPMDEPKTVADIPEEPYPIASTFEWWTPNMEAADDIHAIYELLRDNYVEDDDSMFRFNYSEEFLQWALCPPNYIPDWHVAVRRKADKKLLAFIAGVPVTLRMGTPKYMKVKAQEKGEGEEAAKYDEPRHICEINFLCVHKQLREKRLAPILIKEATRRVNRTNVWQAVYTAGVLLPTPYASGQYFHRSLNPEKLVEIRFSGIPAQYQKFQNPMAMLKRNYQLPSAPKNSGLREMKPSDVPQVRRILMNYLDSFDVGPVFSDAEISHYLLPRDGVVFTYVVENDKKVTDFFSFYRIPSTVIGNSNYNLLNAAYVHYYAATSIPLHQLILDLLIVAHSRGFDVCNMVEILDNRSFVEQLKFGAGDGHLRYYFYNWAYPKIKPSQVALVML 421
                                    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       330       340       350       360       370       380       390       400       410       420
   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 4CYN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q4Q5S8_LEIMA | Q4Q5S8)
molecular function
    GO:0004379    glycylpeptide N-tetradecanoyltransferase activity    Catalysis of the reaction: tetradecanoyl-CoA + glycyl-peptide = CoA + N-tetradecanoylglycyl-peptide.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
    GO:0018008    N-terminal peptidyl-glycine N-myristoylation    The myristoylation of the N-terminal glycine of proteins to form the derivative N-myristoyl-glycine.
    GO:0006499    N-terminal protein myristoylation    The covalent attachment of a myristoyl group to the N-terminal amino acid residue of a protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    A6M  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MYA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Pro A:209 - Thr A:210   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  4cyn
    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
  Q4Q5S8_LEIMA | Q4Q5S8
    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)
  2.3.1.97
    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
  Q4Q5S8_LEIMA | Q4Q5S8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q4Q5S8_LEIMA | Q4Q5S8: 2wsa 3h5z 4a2z 4a30 4a31 4a32 4a33 4c7h 4c7i 4cgl 4cgm 4cgn 4cgo 4cgp 4cyo 4cyp 4cyq 4ucm 4ucn 4ucp 5a27 5a28 5ag4 5ag5 5ag6 5ag7 5age 5g20 5g21

(-) Related Entries Specified in the PDB File

4cyo LEISHMANIA MAJOR N-MYRISTOYLTRANSFERASE IN COMPLEX WITH A HYBRID INHIBITOR (COMPOUND 21).
4cyp LEISHMANIA MAJOR N-MYRISTOYLTRANSFERASE IN COMPLEX WITH A PYRROLIDINE INHIBITOR.
4cyq LEISHMANIA MAJOR N-MYRISTOYLTRANSFERASE IN COMPLEX WITH A HYBRID INHIBITOR (COMPOUND 45).