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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI AMINOPEPTIDASE N IN COMPLEX WITH L-LEUCINE
 
Authors :  A. Addlagatta, R. Gumpena
Date :  16 Jan 15  (Deposition) - 27 Jan 16  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Addlagatta, R. Gumpena
Crystal Structure Of E. Coli Aminopeptidase N In Complex With L-Leucine
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - AMINOPEPTIDASE N
    Chains: A
    EC Number: 3.4.11.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 5-870
    Gene: PEPN, B0932, JW0915
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333
    Strain: K12
    Synonym: ALPHA-AMINOACYLPEPTIDE HYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 17)

Asymmetric/Biological Unit (5, 17)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2LEU1Mod. Amino AcidLEUCINE
3MLI3Ligand/IonMALONATE ION
4NA11Ligand/IonSODIUM ION
5ZN1Ligand/IonZINC ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:297 , HIS A:301 , GLU A:320 , LEU A:902binding site for residue ZN A 901
02AC2SOFTWAREGLN A:119 , GLU A:121 , MET A:260 , ALA A:262 , MET A:263 , GLU A:264 , HIS A:297 , GLU A:298 , HIS A:301 , LYS A:319 , GLU A:320 , TYR A:376 , TYR A:381 , ZN A:901 , MLI A:917 , HOH A:1338 , HOH A:1512binding site for residue LEU A 902
03AC3SOFTWARESER A:332 , ASP A:333 , GLY A:335 , HOH A:1643 , HOH A:1830 , HOH A:1907binding site for residue NA A 903
04AC4SOFTWAREASP A:452 , NA A:909 , HOH A:1721 , HOH A:1881 , HOH A:1900binding site for residue NA A 904
05AC5SOFTWAREHIS A:771 , PHE A:774 , HOH A:1198 , HOH A:1543 , HOH A:1760 , HOH A:1921binding site for residue NA A 905
06AC6SOFTWAREALA A:102 , HOH A:1147 , HOH A:1798 , HOH A:1864 , HOH A:2151binding site for residue NA A 906
07AC7SOFTWARETYR A:544 , HOH A:1534 , HOH A:1752 , HOH A:1869 , HOH A:2046binding site for residue NA A 907
08AC8SOFTWAREGLU A:123 , GLU A:371 , HOH A:1117 , HOH A:1353 , HOH A:1517 , HOH A:1627 , HOH A:1888binding site for residue NA A 908
09AC9SOFTWAREASP A:452 , TYR A:544 , NA A:904 , HOH A:1317 , HOH A:1832 , HOH A:1900 , HOH A:1916binding site for residue NA A 909
10AD1SOFTWAREGLU A:426 , ASP A:432 , SER A:434 , HOH A:1320 , HOH A:1901binding site for residue NA A 910
11AD2SOFTWAREGLN A:19 , ILE A:20 , LEU A:138 , HOH A:1761 , HOH A:1963binding site for residue NA A 911
12AD3SOFTWARETYR A:131 , LEU A:132 , ARG A:134 , VAL A:137 , PRO A:183 , CYS A:184binding site for residue NA A 912
13AD4SOFTWAREGLN A:164 , TYR A:454 , HOH A:1014 , HOH A:1568 , HOH A:1772binding site for residue NA A 913
14AD5SOFTWAREMET A:260 , TYR A:376 , GLU A:382 , ARG A:825 , HOH A:1157binding site for residue GOL A 914
15AD6SOFTWAREARG A:641 , GLU A:642 , THR A:645 , ARG A:686 , ALA A:722 , HOH A:1086 , HOH A:1186 , HOH A:1267 , HOH A:1658 , HOH A:1664 , HOH A:1746binding site for residue MLI A 915
16AD7SOFTWAREASN A:259 , LYS A:274 , ASN A:780 , ARG A:783 , HOH A:1038 , HOH A:1075 , HOH A:1171 , HOH A:1679binding site for residue MLI A 916
17AD8SOFTWAREARG A:293 , HIS A:297 , GLU A:298 , ASP A:327 , TYR A:381 , LEU A:902 , HOH A:1385 , HOH A:1512binding site for residue MLI A 917

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XO3)

(-) 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 4XO3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XO3)

(-) Exons   (0, 0)

(no "Exon" information available for 4XO3)

(-) 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:867
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               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...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xo3 A   5 PQAKYRHDYRAPDYQITDIDLTFDLDAQKTVVTAVSQAVRHGASDAPLRLNGEDLKLVSVHINDEPWTAWKEEEGALVISNLPERFTLKIINEISPAANTALEGLYQSGDALCTQCEAEGFRHITYYLDRPDVLARFTTKIIADKIKYPFLLSNGNRVAQGELENGRHWVQWQDPFPKPCYLFALVAGDFDVLRDTFTTRSGREVALELYVDRGNLDRAPWAMTSLKNSMKWDEERFGLEYDLDIYMIVAVDFFNMGAMENKGLNIFNSKYVLARTDTATDKDYLDIERVIGHEYFHNWTGNRVTCRDWFQLSLKEGLTVFRDQEFSSDLGSRAVNRINNVRTMRGLQFAEDASPMAHPIRPDMVIEMNNFYTLTVYEKGAEVIRMIHTLLGEENFQKGMQLYFERHDGSAATCDDFVQAMEDASNVDLSHFRRWYSQSGTPIVTVKDDYNPETEQYTLTISQRTPATPDQAEKQPLHIPFAIELYDNEGKVIPLQKGGHPVNSVLNVTQAEQTFVFDNVYFQPVPALLCEFSAPVKLEYKWSDQQLTFLMRHARNDFSRWDAAQSLLATYIKLNVARHQQGQPLSLPVHVADAFRAVLLDEKIDPALAAEILTLPSVNEMAELFDIIDPIAIAEVREALTRTLATELADELLAIYNANYQSEYRVEHEDIAKRTLRNACLRFLAFGETHLADVLVSKQFHEANNMTDALAALSAAVAAQLPCRDALMQEYDDKWHQNGLVMDKWFILQATSPAANVLETVRGLLQHRSFTMSNPNRIRSLIGAFAGSNPAAFHAEDGSGYLFLVEMLTDLNSRNPQVASRLIEPLIRLKRYDAKRQEKMRAALEQLKGLENLSGDLYEKITKALAL 902
                                    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     ||
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           870|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            902
   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 4XO3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XO3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XO3)

(-) 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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 Related Entries

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UniProtKB/Swiss-Prot
        AMPN_ECOLI | P04825: 2dq6 2dqm 2hpo 2hpt 2zxg 3b2p 3b2x 3b34 3b37 3b3b 3ked 3puu 3qjx 4q4e 4q4i 4xmt 4xmu 4xmv 4xmw 4xmx 4xmz 4xn1 4xn2 4xn4 4xn5 4xn7 4xn8 4xn9 4xna 4xnb 4xnd 4xo4 4xo5 5mfr 5mfs 5mft

(-) Related Entries Specified in the PDB File

4xms 4xmt 4xmu 4xmv 4xmw 4xmx 4xmz 4xn1 4xn2 4xn4 4xn5 4xn7 4xn8 4xn9 4xna 4xnb 4xnd 4xo4 4xo5