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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI AMINOPEPTIDASE N IN COMPLEX WITH L-BETA HOMOTRYPTOPHAN
 
Authors :  A. Addlagatta, R. Gumpena
Date :  15 Jan 15  (Deposition) - 02 Mar 16  (Release) - 02 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
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-Beta Homotryptophan
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - AMINOPEPTIDASE N
    ChainsA
    EC Number3.4.11.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 5-870
    GenePEPN, B0932, JW0915
    Organism ScientificESCHERICHIA COLI K-12
    Organism Taxid83333
    StrainK12
    SynonymALPHA-AMINOACYLPEPTIDE HYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 46)

Asymmetric/Biological Unit (5, 46)
No.NameCountTypeFull Name
1GOL22Ligand/IonGLYCEROL
2HT71Ligand/Ion(3S)-3-AMINO-4-(1H-INDOL-3-YL)BUTANOIC ACID
3MLI14Ligand/IonMALONATE ION
4NA8Ligand/IonSODIUM ION
5ZN1Ligand/IonZINC ION

(-) Sites  (46, 46)

Asymmetric Unit (46, 46)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:297 , HIS A:301 , GLU A:320 , HT7 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 , ASN A:373 , TYR A:381 , ZN A:901 , MLI A:941 , HOH A:1501binding site for residue HT7 A 902
03AC3SOFTWAREGLN A:19 , ILE A:20 , LEU A:138 , HOH A:1549 , HOH A:1753binding site for residue NA A 903
04AC4SOFTWAREASP A:452 , GOL A:932 , MLI A:946 , HOH A:1001 , HOH A:1664binding site for residue NA A 904
05AC5SOFTWAREASN A:399 , SER A:429 , HOH A:1419 , HOH A:1552 , HOH A:1665 , HOH A:1694binding site for residue NA A 905
06AC6SOFTWAREASN A:344 , GLU A:382 , HOH A:1079 , HOH A:1161 , HOH A:1339 , HOH A:1344binding site for residue NA A 906
07AC7SOFTWARESER A:332 , ASP A:333 , GLY A:335 , MLI A:936 , HOH A:1177 , HOH A:1648binding site for residue NA A 907
08AC8SOFTWAREGLY A:350 , ASN A:623 , HOH A:1028 , HOH A:1223 , HOH A:1645binding site for residue NA A 908
09AC9SOFTWAREASN A:67 , THR A:91 , HOH A:1710 , HOH A:1724 , HOH A:1745binding site for residue NA A 909
10AD1SOFTWARELEU A:551 , SER A:570 , THR A:574 , GOL A:921 , HOH A:1328 , HOH A:1390 , HOH A:1469binding site for residue NA A 910
11AD2SOFTWAREALA A:531 , LEU A:532 , TRP A:546 , SER A:563 , ASP A:566 , ALA A:567 , SER A:570binding site for residue GOL A 911
12AD3SOFTWARELYS A:8 , GLU A:123 , ASP A:312 , TRP A:313 , PHE A:314 , HOH A:1057 , HOH A:1334 , HOH A:1395 , HOH A:1568binding site for residue GOL A 912
13AD4SOFTWARETHR A:72 , TRP A:74 , VAL A:670 , GLU A:671 , GOL A:915 , HOH A:1502binding site for residue GOL A 913
14AD5SOFTWAREGLU A:69 , PRO A:70 , TRP A:71 , THR A:72 , ASP A:221 , PRO A:224 , ALA A:278 , TYR A:288 , HOH A:1077binding 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:913 , MLI A:934 , HOH A:1347binding site for residue GOL A 915
16AD7SOFTWAREASN A:623 , GLY A:791 , MLI A:933 , HOH A:1198 , HOH A:1243binding site for residue GOL A 916
17AD8SOFTWAREGLU A:292 , VAL A:670 , HIS A:672 , HOH A:1014 , HOH A:1502binding site for residue GOL A 917
18AD9SOFTWAREARG A:681 , GLN A:703 , ALA A:707 , ASN A:708 , ASN A:709 , ASP A:712 , HOH A:1069 , HOH A:1521binding site for residue GOL A 918
19AE1SOFTWARETHR A:755 , PRO A:757 , SER A:792 , ASN A:793 , HOH A:1119 , HOH A:1433binding site for residue GOL A 919
20AE2SOFTWAREMET A:260 , GLY A:261 , LYS A:274 , TYR A:275 , ARG A:783 , ARG A:825 , MLI A:941 , MLI A:942binding site for residue GOL A 920
21AE3SOFTWAREARG A:207 , GLU A:208 , ASP A:248 , LYS A:545 , TRP A:546 , THR A:574 , NA A:910 , HOH A:1007 , HOH A:1091 , HOH A:1390 , HOH A:1469binding site for residue GOL A 921
22AE4SOFTWAREVAL A:162 , GLN A:177 , GLN A:549 , HOH A:1009 , HOH A:1035binding site for residue GOL A 922
23AE5SOFTWARELYS A:144 , GLN A:175 , ASN A:492binding site for residue GOL A 923
24AE6SOFTWARESER A:441 , GLN A:442 , GLU A:477 , GLN A:479 , HOH A:1181 , HOH A:1374binding site for residue GOL A 924
25AE7SOFTWAREASN A:232 , TRP A:236 , GLU A:239 , HOH A:1014 , HOH A:1059binding site for residue GOL A 925
26AE8SOFTWAREGLU 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:1179 , HOH A:1300binding site for residue GOL A 926
27AE9SOFTWARELEU A:617 , THR A:618 , LEU A:619 , ARG A:641 , THR A:645 , ALA A:683 , ARG A:686 , PHE A:687 , MLI A:939 , HOH A:1173binding site for residue GOL A 927
28AF1SOFTWARELEU A:289 , ASN A:343 , GLU A:615 , ILE A:675 , THR A:679 , HOH A:1027 , HOH A:1155 , HOH A:1584binding site for residue GOL A 928
29AF2SOFTWAREPRO A:16 , ASP A:17 , TYR A:18 , ARG A:53 , ARG A:134 , HOH A:1056 , HOH A:1093binding site for residue GOL A 929
30AF3SOFTWAREASN A:160 , ASP A:246 , LEU A:247 , ASP A:248 , SER A:547 , ASP A:548 , GLN A:549 , HOH A:1091binding site for residue GOL A 930
31AF4SOFTWAREASP A:68 , GLU A:69 , THR A:280 , ASP A:281 , ASN A:708binding site for residue GOL A 931
32AF5SOFTWAREASP A:452 , TYR A:461 , GLN A:527 , PRO A:528 , TYR A:544 , GLN A:550 , NA A:904 , MLI A:946 , HOH A:1064 , HOH A:1688binding site for residue GOL A 932
33AF6SOFTWAREALA A:354 , ILE A:632 , ARG A:832 , ARG A:835 , TYR A:836 , GOL A:916 , HOH A:1028 , HOH A:1120 , HOH A:1261binding site for residue MLI A 933
34AF7SOFTWARELEU A:61 , VAL A:62 , TRP A:74 , ARG A:669 , GLU A:671 , GOL A:915 , HOH A:1392binding site for residue MLI A 934
35AF8SOFTWAREASP A:28 , LYS A:33 , ARG A:171binding site for residue MLI A 935
36AF9SOFTWAREGLY A:335 , SER A:336 , ARG A:337 , ALA A:338 , NA A:907 , HOH A:1177 , HOH A:1463 , HOH A:1581binding site for residue MLI A 936
37AG1SOFTWAREHIS A:11 , ARG A:14 , GLN A:467 , ARG A:468 , THR A:469 , LYS A:478 , GLN A:479 , PRO A:480 , HOH A:1244 , HOH A:1336binding site for residue MLI A 937
38AG2SOFTWAREASN A:579 , HIS A:583 , GLN A:587 , LEU A:589 , GLU A:639 , VAL A:640 , ALA A:643binding site for residue MLI A 938
39AG3SOFTWAREARG A:641 , GLU A:642 , THR A:645 , ARG A:686 , ALA A:722 , GOL A:927 , HOH A:1023 , HOH A:1119binding site for residue MLI A 939
40AG4SOFTWAREGLN A:111 , GLY A:113 , PHE A:257 , SER A:777 , HOH A:1126 , HOH A:1144 , HOH A:1276binding site for residue MLI A 940
41AG5SOFTWAREGLY A:261 , ARG A:293 , GLU A:298 , TYR A:381 , HT7 A:902 , GOL A:920 , MLI A:942 , HOH A:1065 , HOH A:1225binding site for residue MLI A 941
42AG6SOFTWARETYR A:376 , THR A:377 , LEU A:378 , TYR A:381 , GLU A:382 , ARG A:825 , GOL A:920 , MLI A:941 , HOH A:1214 , HOH A:1373binding site for residue MLI A 942
43AG7SOFTWAREGLY A:396 , GLU A:397 , GLU A:398 , HOH A:1002 , HOH A:1048binding site for residue MLI A 943
44AG8SOFTWAREMET A:555 , ARG A:556 , ARG A:564 , VAL A:602 , ASP A:605 , HOH A:1411binding site for residue MLI A 944
45AG9SOFTWAREGLU A:239 , ARG A:240 , PHE A:241 , GLN A:401 , GLN A:405 , GLN A:585 , GLN A:587 , HOH A:1005 , HOH A:1491binding site for residue MLI A 945
46AH1SOFTWAREASP A:452 , TYR A:544 , LYS A:545 , GLN A:550 , NA A:904 , GOL A:932 , HOH A:1001 , HOH A:1017 , HOH A:1415binding site for residue MLI A 946

(-) SS Bonds  (0, 0)

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

(-) 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 4XND)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XND)

(-) 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.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeehhhhhhhhhhhhhh......hhhhhh....eeeeeeeee....eeeeeeeee..............eeeeeeee.........ee..ee...eeee...eeeeee.......eeee........eee...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh...hhhhhhhhh...hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xnd 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 4XND)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 | P048252dq6 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 4xo3 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 4xo3 4xo4 4xo5