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(-) Description

Title :  CRYSTAL STRUCTURE OF E.COLI AMINOPEPTIDASE N IN COMPLEX WITH AMASTATIN
 
Authors :  R. Reddi, R. J. Ganji, A. Addlagatta
Date :  14 Apr 14  (Deposition) - 15 Apr 15  (Release) - 15 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Aminopeptidase, Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. J. Ganji, R. Reddi, R. Gumpena, A. K. Marapaka, T. Arya, P. Sankoju, S. Bhukya, A. Addlagatta
Structural Basis For The Inhibition Of M1 Family Aminopeptidases By The Natural Product Actinonin: Crystal Structure In Complex With E. Coli Aminopeptidase N
Protein Sci. 2015
PubMed-ID: 25644575  |  Reference-DOI: 10.1002/PRO.2653

(-) Compounds

Molecule 1 - AMINOPEPTIDASE N
    Chains: A
    EC Number: 3.4.11.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PEPN, B0932, JW0915
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: ALPHA-AMINOACYLPEPTIDE HYDROLASE
 
Molecule 2 - AMASTATIN
    Chains: C
    Engineered: YES
    Organism Scientific: STREPTOMYCES SP. ME98-M3
    Organism Taxid: 1883
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2L2O1Mod. Amino Acid(2S,3R)-3-AMINO-2-HYDROXY-5-METHYLHEXANOIC ACID
3NA3Ligand/IonSODIUM ION
4ZN1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:297 , HIS A:301 , GLU A:320 , L2O C:1BINDING SITE FOR RESIDUE ZN A 901
02AC2SOFTWARESER A:332 , ASP A:333 , GLY A:335 , HOH A:1284BINDING SITE FOR RESIDUE NA A 902
03AC3SOFTWAREARG A:161 , ASP A:452 , HOH A:1176 , HOH A:1387BINDING SITE FOR RESIDUE NA A 903
04AC4SOFTWAREGLN A:19 , ILE A:20 , LEU A:138 , HOH A:1158 , HOH A:1224BINDING SITE FOR RESIDUE NA A 904
05AC5SOFTWARELEU A:532 , TRP A:546 , ASP A:566 , ALA A:567 , SER A:570 , HOH A:1125BINDING SITE FOR RESIDUE GOL A 905
06AC6SOFTWARESER A:63 , VAL A:64 , TRP A:71 , TRP A:74 , ARG A:669 , VAL A:670 , GLU A:671 , GOL A:907 , HOH A:1441BINDING SITE FOR RESIDUE GOL A 906
07AC7SOFTWARETHR A:72 , TRP A:74 , VAL A:670 , GOL A:906BINDING SITE FOR RESIDUE GOL A 907
08AC8SOFTWAREARG A:681 , ALA A:707 , ASN A:708 , ASN A:709 , ASP A:712 , HOH A:1256 , HOH A:1389BINDING SITE FOR RESIDUE GOL A 908
09AC9SOFTWAREGLU A:409 , ASP A:412 , SER A:590 , LEU A:591 , HOH A:1475BINDING SITE FOR RESIDUE GOL A 909
10BC1SOFTWAREGLN A:119 , GLU A:121 , ASN A:259 , MET A:260 , GLY A:261 , ALA A:262 , MET A:263 , GLU A:264 , LYS A:274 , TYR A:275 , HIS A:297 , GLU A:298 , HIS A:301 , LYS A:319 , GLU A:320 , TYR A:376 , TYR A:381 , ARG A:783 , ARG A:825 , ZN A:901 , HOH C:101BINDING SITE FOR CHAIN C OF AMASTATIN

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q4I)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:121 -Ala A:122

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q4I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q4I)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q4I)

(-) 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:866
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.hhh....eeeeeeeeeee.....eeeeeeeeeee.......eeee....eeeeeee..ee...eeee..eeee.....eeeeeeeeeehhhhh....eeeee..eeeee....hhhhh...........eeeeeeeee.....eeee..eeeeeee....eeeeeee.....hhhhh.eeee..eeeeeeee.....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee......ee....eeeee.hhh.......hhhhhhhhhhhhhhhhhh......eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeehhhhhhhhhhhhhh......hhhhhh....eeeeeeeee....eeeeeeeee..............eeeeeeee.........ee..ee...eeee...eeeeee.......eeee........eee...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh...hhhhhhhhh...hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q4i A   5 PQAKYRHDYRAPDYQITDIDLTFDLDAQKTVVTAVSQAVRHGASDAPLRLNGEDLKLVSVHINDEPWTAWKEEEGALVISNLPERFTLKIINEISPAANTALEGLYQSGDALCTQCEAEGFRHITYYLDRPDVLARFTTKIIADKIKYPFLLSNGNRVAQGELENGRHWVQWQDPFPKPCYLFALVAGDFDVLRDTFTTRSGREVALELYVDRGNLDRAPWAMTSLKNSMKWDEERFGLEYDLDIYMIVAVDFFNMGAMENKGLNIFNSKYVLARTDTATDKDYLDIERVIGHEYFHNWTGNRVTCRDWFQLSLKEGLTVFRDQEFSSDLGSRAVNRINNVRTMRGLQFAEDASPMAHPIRPDMVIEMNNFYTLTVYEKGAEVIRMIHTLLGEENFQKGMQLYFERHDGSAATCDDFVQAMEDASNVDLSHFRRWYSQSGTPIVTVKDDYNPETEQYTLTISQRTPATPDQAEKQPLHIPFAIELYDNEGKVIPLQKGGHPVNSVLNVTQAEQTFVFDNVYFQPVPALLCEFSAPVKLEYKWSDQQLTFLMRHARNDFSRWDAAQSLLATYIKLNVARHQQGQPLSLPVHVADAFRAVLLDEKIDPALAAEILTLPSVNEMAELFDIIDPIAIAEVREALTRTLATELADELLAIYNANYQSEYRVEHEDIAKRTLRNACLRFLAFGETHLADVLVSKQFHEANNMTDALAALSAAVAAQLPCRDALMQEYDDKWHQNGLVMDKWFILQATSPAANVLETVRGLLQHRSFTMSNPNRIRSLIGAFAGSNPAAFHAEDGSGYLFLVEMLTDLNSRNPQVASRLIEPLIRLKRYDAKRQEKMRAALEQLKGLENLSGDLYEKITKALA 870
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864      


Chain C from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 4q4i C   1 xVVD   4
                            |   
                            1-L2O
   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 4Q4I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q4I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q4I)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu A:121 - Ala A:122   [ RasMol ]  
 

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        AMPN_ECOLI | P04825: 2dq6 2dqm 2hpo 2hpt 2zxg 3b2p 3b2x 3b34 3b37 3b3b 3ked 3puu 3qjx 4q4e 4xmt 4xmu 4xmv 4xmw 4xmx 4xmz 4xn1 4xn2 4xn4 4xn5 4xn7 4xn8 4xn9 4xna 4xnb 4xnd 4xo3 4xo4 4xo5 5mfr 5mfs 5mft

(-) Related Entries Specified in the PDB File

4q4e