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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI AMINOPEPTIDASE N IN COMPLEX WITH L-2,3-DIAMINOPROPIONIC ACID
 
Authors :  A. Addlagatta, R. Gumpena
Date :  15 Jan 15  (Deposition) - 02 Mar 16  (Release) - 02 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.22
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-2, 3-Diaminopropionic Acid
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, 36)

Asymmetric/Biological Unit (5, 36)
No.NameCountTypeFull Name
1DPP1Ligand/IonDIAMINOPROPANOIC ACID
2GOL28Ligand/IonGLYCEROL
3MLI2Ligand/IonMALONATE ION
4NA4Ligand/IonSODIUM ION
5ZN1Ligand/IonZINC ION

(-) Sites  (36, 36)

Asymmetric Unit (36, 36)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:297 , HIS A:301 , GLU A:320 , DPP A:902binding site for residue ZN A 901
02AC2SOFTWAREGLU A:121 , 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:381 , ZN A:901 , HOH A:1032 , HOH A:1039binding site for residue DPP A 902
03AC3SOFTWARESER A:332 , ASP A:333 , GLY A:335 , HOH A:1332 , HOH A:1371binding site for residue NA A 903
04AC4SOFTWAREASP A:452 , GOL A:924 , HOH A:1344 , HOH A:1419binding site for residue NA A 904
05AC5SOFTWAREGLY A:350 , ALA A:354 , ASN A:623 , GLU A:627 , HOH A:1392binding site for residue NA A 905
06AC6SOFTWAREGLN A:19 , ILE A:20 , LEU A:138 , HOH A:1338binding site for residue NA A 906
07AC7SOFTWARELEU A:532 , TRP A:546 , ASP A:566 , ALA A:567 , SER A:570binding site for residue GOL A 907
08AC8SOFTWARETYR A:376 , GLU A:382 , GOL A:933binding site for residue GOL A 908
09AC9SOFTWARETHR A:72 , TRP A:74 , VAL A:670 , GLU A:671 , GOL A:915 , HOH A:1072binding site for residue GOL A 909
10AD1SOFTWAREGLU A:69 , PRO A:70 , TRP A:71 , THR A:72 , PRO A:224 , ALA A:278 , TYR A:288 , HOH A:1076binding site for residue GOL A 910
11AD2SOFTWAREHIS A:11 , GLN A:467 , THR A:469 , LYS A:478 , PRO A:480binding site for residue GOL A 911
12AD3SOFTWAREMET A:360 , ALA A:361 , HIS A:362 , ASP A:367 , MET A:368 , PHE A:375 , LYS A:867 , GOL A:913 , HOH A:1118binding site for residue GOL A 912
13AD4SOFTWAREPRO A:363 , ASP A:367 , ASP A:474 , GLN A:475 , ALA A:476 , GOL A:912 , GOL A:914 , HOH A:1333binding site for residue GOL A 913
14AD5SOFTWAREPRO A:473 , ASP A:474 , ALA A:476 , GOL A:913 , HOH A:1029 , HOH A:1154binding site for residue GOL A 914
15AD6SOFTWARESER A:63 , VAL A:64 , TRP A:71 , TRP A:74 , ARG A:669 , VAL A:670 , GLU A:671 , GOL A:909 , MLI A:936 , HOH A:1169binding site for residue GOL A 915
16AD7SOFTWARELYS A:834 , ARG A:845 , LYS A:852 , TYR A:862 , ALA A:870binding site for residue GOL A 916
17AD8SOFTWARELEU A:617 , THR A:618 , LEU A:619 , ARG A:641 , THR A:645 , ALA A:683 , ARG A:686 , PHE A:687 , GOL A:930 , HOH A:1207binding site for residue GOL A 917
18AD9SOFTWAREPHE A:180 , PRO A:181 , ARG A:307 , ASP A:412 , GLY A:413 , PRO A:592 , VAL A:593 , HIS A:594 , HOH A:1149binding site for residue GOL A 918
19AE1SOFTWAREARG A:204 , GLU A:238 , GLU A:244 , ALA A:581 , ARG A:582 , GLN A:585 , GLN A:587 , HOH A:1038binding site for residue GOL A 919
20AE2SOFTWARELEU A:29 , ASP A:30 , ALA A:31 , ALA A:147 , ASP A:148 , TYR A:152 , ARG A:171 , HOH A:1001binding site for residue GOL A 920
21AE3SOFTWAREGLU A:123 , TRP A:313 , PHE A:314 , HOH A:1093 , HOH A:1097 , HOH A:1273binding site for residue GOL A 921
22AE4SOFTWAREARG A:10 , HIS A:11 , ARG A:311 , HOH A:1276binding site for residue GOL A 922
23AE5SOFTWAREGLN A:442 , GLN A:475 , GLU A:477binding site for residue GOL A 923
24AE6SOFTWAREARG A:161 , ASP A:452 , PRO A:528 , NA A:904 , HOH A:1008 , HOH A:1269binding site for residue GOL A 924
25AE7SOFTWAREVAL A:162 , GLN A:177 , GLN A:549 , PHE A:553 , HOH A:1046 , HOH A:1082binding site for residue GOL A 925
26AE8SOFTWARESER A:336 , ASN A:340 , HIS A:672 , GOL A:934 , HOH A:1009 , HOH A:1346binding site for residue GOL A 926
27AE9SOFTWAREASN A:623 , ILE A:632 , HIS A:798 , PRO A:829 , ARG A:832 , TYR A:836 , HOH A:1234 , HOH A:1286binding site for residue GOL A 927
28AF1SOFTWARETYR A:664 , ARG A:681 , GLN A:703 , ALA A:707 , ASN A:708 , ASP A:712 , HOH A:1035binding site for residue GOL A 928
29AF2SOFTWAREASP A:58 , LYS A:60 , GLU A:97 , SER A:99binding site for residue GOL A 929
30AF3SOFTWAREALA A:638 , ARG A:641 , ARG A:686 , PHE A:690 , GOL A:917 , HOH A:1064 , HOH A:1456binding site for residue GOL A 930
31AF4SOFTWAREARG A:728 , GLN A:753 , SER A:756 , ALA A:758 , ASN A:760 , THR A:764binding site for residue GOL A 931
32AF5SOFTWAREGLU A:244 , TYR A:245 , ASP A:246 , TRP A:303 , ARG A:307 , LEU A:578 , SER A:590 , LEU A:591 , PRO A:592 , HOH A:1025 , HOH A:1051binding site for residue GOL A 932
33AF6SOFTWAREGLY A:261 , LYS A:274 , TYR A:275 , ARG A:783 , ARG A:825 , GOL A:908binding site for residue GOL A 933
34AF7SOFTWARELEU A:289 , THR A:679 , GOL A:926 , HOH A:1136 , HOH A:1225 , HOH A:1346binding site for residue GOL A 934
35AF8SOFTWAREASN A:623 , GLY A:791 , SER A:792 , HOH A:1275binding site for residue MLI A 935
36AF9SOFTWARELEU A:61 , VAL A:62 , TRP A:74 , ARG A:669 , GLU A:671 , GOL A:915 , HOH A:1254binding site for residue MLI A 936

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XN7)

(-) 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 4XN7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XN7)

(-) Exons   (0, 0)

(no "Exon" information available for 4XN7)

(-) 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..........eeeeeeeeee.....eeee..eeeeeee....eeeeeeeeeeeehhhhh.eeee..eeeeeeee.....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee......ee....eeeee.hhh.......hhhhhhhhhhhhhhhhhh......eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeehhhhhhhhhhhhhh......hhhhhh....eeeeeeeee....eeeeeeeee..............eeeeeeee.........ee..ee...eeee...eeeeee.......eeee.hhhh...eee...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh....hhhhhhhhh...hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xn7 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
   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 4XN7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XN7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XN7)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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

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 4xn8 4xn9 4xna 4xnb 4xnd 4xo3 4xo4 4xo5 5mfr 5mfs 5mft

(-) Related Entries Specified in the PDB File

4xms 4xmt 4xmu 4xmv 4xmw 4xmx 4xmz 4xn1 4xn2 4xn4 4xn5 4xn8 4xn9 4xna 4xnb 4xnd 4xo3 4xo4 4xo5