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(-) Description

Title :  CRYSTAL STRUCTURE OF TRUNCATED (DELTA 1-89) HUMAN METHIONINE AMINOPEPTIDASE TYPE 1 IN COMPLEX WITH 2-((5-CHLORO-6-METHYL-2-(PYRIDIN-2-YL)PYRIMIDIN-4-YL)AMINO)-3-PHENYLPROPANAMIDE
 
Authors :  A. Addlagatta, C. Kishor, T. Arya
Date :  28 Dec 12  (Deposition) - 11 Dec 13  (Release) - 11 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Pita-Bread Fold, Aminopeptidase, Ribosome, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Kishor, T. Arya, R. Reddi, X. Chen, V. Saddanapu, A. K. Marapaka, R. Gumpena, D. Ma, J. O. Liu, A. Addlagatta
Identification, Biochemical And Structural Evaluation Of Species-Specific Inhibitors Against Type I Methionine Aminopeptidases
J. Med. Chem. V. 56 5295 2013
PubMed-ID: 23767698  |  Reference-DOI: 10.1021/JM400395P

(-) Compounds

Molecule 1 - METHIONINE AMINOPEPTIDASE 1
    ChainsA
    EC Number3.4.11.18
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21 (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 81-384
    GeneMETAP1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMAP 1, METAP 1, PEPTIDASE M 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CO3Ligand/IonCOBALT (II) ION
2K1Ligand/IonPOTASSIUM ION
3SHX1Ligand/IonNALPHA-[5-CHLORO-6-METHYL-2-(PYRIDIN-2-YL)PYRIMIDIN-4-YL]-D-PHENYLALANINAMIDE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:195 , TYR A:196 , CYS A:203 , HIS A:212 , TYR A:300 , HIS A:310 , TRP A:353 , CO A:404 , HOH A:501 , HOH A:567 , HOH A:660BINDING SITE FOR RESIDUE SHX A 401
2AC2SOFTWAREASP A:240 , HIS A:303 , THR A:334 , GLU A:336 , GLU A:367 , CO A:403 , HOH A:578BINDING SITE FOR RESIDUE CO A 402
3AC3SOFTWAREASP A:229 , ASP A:240 , GLU A:367 , CO A:402 , HOH A:528 , HOH A:578BINDING SITE FOR RESIDUE CO A 403
4AC4SOFTWAREHIS A:212 , SHX A:401 , HOH A:501 , HOH A:530 , HOH A:549BINDING SITE FOR RESIDUE CO A 404
5AC5SOFTWARESER A:205 , ASN A:207 , VAL A:209 , SER A:363 , HOH A:513BINDING SITE FOR RESIDUE K A 405

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:100 -Pro A:101
2Ala A:312 -Pro A:313

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IKU)

(-) 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:304
                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................hhhhhh....hhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh..ee...hhhhh....eeee..eee.............eeeeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..ee.....eee......eeeee................eeee..eee.....eee......eee.....eee..eeeeee..eeee.........hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iku A  90 YRYTGKLRPHYPLMPTRPVPSYIQRPDYADHPLGMSESEQALKGTSQIKLLSSEDIEGMRLVCRLAREVLDVAAGMIKPGVTTEEIDHAVHLACIARNCYPSPLNYYNFPKSCCTSVNEVICHGIPDRRPLQEGDIVNVDITLYRNGYHGDLNETFFVGEVDDGARKLVQTTYECLMQAIDAVKPGVRYRELGNIIQKHAQANGFSVVRSYCGHGIHKLFHTAPNVPHYAKNKAVGVMKSGHVFTIEPMICEGGWQDETWPDGWTAVTRDGKRSAQFEHTLLVTDTGCEILTRRLDSARPHFMS 393
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389    

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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 4IKU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:312 - Pro A:313   [ RasMol ]  
    Tyr A:100 - Pro A:101   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        MAP11_HUMAN | P535822b3h 2b3k 2b3l 2g6p 2gz5 2nq6 2nq7 4fli 4flj 4flk 4fll 4hxx 4ikr 4iks 4ikt 4iu6 4u1b 4u69 4u6c 4u6e 4u6j 4u6w 4u6z 4u70 4u71 4u73 4u75 4u76

(-) Related Entries Specified in the PDB File

2g6p SAME PROTEIN IN COMPLEX WITH 5-CHLORO-6-METHYL-N-(2- PHENYLETHYL)-2-PYRIDIN- 2-YLPYRIMIDIN-4-AMINE
4ikr SAME PROTEIN IN COMPLEX WITH 2-(4-(5-CHLORO-6-METHYL-2- (PYRIDIN-2-YL)PYRIMIDIN-4-YL)PIPERAZIN-1-YL)ETHANOL
4iks SAME PROTEIN IN COMPLEX WITH N1-(5-CHLORO-6-METHYL-2- (PYRIDIN-2-YL)PYRIMIDIN-4-YL)-N2-(6-(TRIFLUOROMETHYL) PYRIDIN-2-YL)ETHANE-1,2-DIAMINE
4ikt SAME PROTEIN IN COMPLEX WITH N1-(5-CHLORO-6-METHYL-2- (PYRIDIN-2-YL)PYRIMIDIN-4-YL)-N2-(5-(TRIFLUOROMETHYL) PYRIDIN-2-YL)ETHANE-1,2-DIAMINE