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Title :  THE CRYSTAL STRUCTURE OF E. COLI AMINOPEPTIDASE N IN COMPLEX WITH 7-AMINO-4-PHENYL-5,7,8,9-TETRAHYDROBENZOCYCLOHEPTEN-6-ONE
 
Authors :  G. Peng, V. Olieric, A. G. Mcewen, C. Schmitt, S. Albrecht, J. Cavarelli
Date :  18 Nov 16  (Deposition) - 19 Apr 17  (Release) - 19 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.57
Chains :  Asym./Biol. Unit :  A
Keywords :  M1 Aminopeptidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Peng, A. G. Mcewen, V. Olieric, C. Schmitt, S. Albrecht, J. Cavarelli, C. Tarnus
Insight Into The Remarkable Affinity And Selectivity Of The Aminobenzosuberone Scaffold For The M1 Aminopeptidases Family Based On Structure Analysis.
Proteins 2017
PubMed-ID: 28383176  |  Reference-DOI: 10.1002/PROT.25301

(-) Compounds

Molecule 1 - AMINOPEPTIDASE N
    Chains: A
    EC Number: 3.4.11.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: PEPN, B0932, JW0915
    Organism Scientific: ESCHERICHIA COLI
    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  (7, 39)

Asymmetric/Biological Unit (7, 39)
No.NameCountTypeFull Name
17ML1Ligand/Ion[(7~{S})-6,6-BIS(OXIDANYL)-4-PHENYL-5,7,8,9-TETRAHYDROBENZO[7]ANNULEN-7-YL]AZANIUM
2CL4Ligand/IonCHLORIDE ION
3DMS5Ligand/IonDIMETHYL SULFOXIDE
4GOL14Ligand/IonGLYCEROL
5MLI5Ligand/IonMALONATE ION
6NA9Ligand/IonSODIUM ION
7ZN1Ligand/IonZINC ION

(-) Sites  (39, 39)

Asymmetric Unit (39, 39)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:297 , HIS A:301 , GLU A:320 , 7ML A:1002binding site for residue ZN A 1001
02AC2SOFTWAREGLU A:121 , MET A:260 , ALA A:262 , GLU A:264 , ARG A:293 , HIS A:297 , GLU A:298 , HIS A:301 , LYS A:319 , GLU A:320 , TYR A:381 , ZN A:1001 , MLI A:1012binding site for residue 7ML A 1002
03AC3SOFTWARESER A:332 , ASP A:333 , GLY A:335 , HOH A:1927 , HOH A:2214 , HOH A:2302binding site for residue NA A 1003
04AC4SOFTWAREHIS A:771 , PHE A:774 , HOH A:1322 , HOH A:1559 , HOH A:2247 , HOH A:2291binding site for residue NA A 1004
05AC5SOFTWARESER A:508 , HOH A:1882 , HOH A:2060 , HOH A:2145 , HOH A:2340 , HOH A:2806binding site for residue NA A 1005
06AC6SOFTWAREGLU A:123 , GLU A:371 , HOH A:1145 , HOH A:1497 , HOH A:1675 , HOH A:1872 , HOH A:2314binding site for residue NA A 1006
07AC7SOFTWAREASP A:452 , TYR A:544 , HOH A:1555 , HOH A:2295 , HOH A:2330 , HOH A:2508binding site for residue NA A 1007
08AC8SOFTWAREGLU A:371 , HOH A:1154 , HOH A:1327 , HOH A:1605 , HOH A:2314 , HOH A:2481binding site for residue NA A 1008
09AC9SOFTWAREASN A:67 , THR A:91 , HOH A:2262 , HOH A:2378 , HOH A:2400 , HOH A:2449binding site for residue NA A 1009
10AD1SOFTWAREASN A:511 , THR A:513 , GLN A:517 , HOH A:1607 , HOH A:2249 , HOH A:2586binding site for residue NA A 1010
11AD2SOFTWAREASP A:452 , HOH A:1293 , HOH A:1843 , HOH A:2225 , HOH A:2265 , HOH A:2783binding site for residue NA A 1011
12AD3SOFTWARETYR A:376 , THR A:377 , LEU A:378 , TYR A:381 , GLU A:382 , ARG A:825 , 7ML A:1002 , GOL A:1038 , HOH A:1160binding site for residue MLI A 1012
13AD4SOFTWARESER A:205 , LYS A:577 , LEU A:628 , PHE A:629 , ASP A:630 , HOH A:1103 , HOH A:1396 , HOH A:2492binding site for residue MLI A 1013
14AD5SOFTWAREALA A:531 , LEU A:532 , TRP A:546 , LEU A:551 , ASP A:566 , ALA A:567 , SER A:570 , HOH A:1133 , HOH A:1175binding site for residue MLI A 1014
15AD6SOFTWAREGLY A:396 , GLU A:397 , GLU A:398 , HOH A:1169 , HOH A:1171 , HOH A:1223 , HOH A:1432 , HOH A:1437 , HOH A:1946 , HOH A:1952 , HOH A:2539binding site for residue MLI A 1015
16AD7SOFTWAREGLU A:123 , TRP A:313 , PHE A:314 , VAL A:369 , MET A:372 , HOH A:1145 , HOH A:1189 , HOH A:1239 , HOH A:1261 , HOH A:1719binding site for residue MLI A 1016
17AD8SOFTWARETHR A:393 , GLU A:535 , HOH A:1214 , HOH A:2077binding site for residue DMS A 1017
18AD9SOFTWAREGLU A:627 , PHE A:629 , ASP A:630 , ARG A:835 , HOH A:1119binding site for residue DMS A 1018
19AE1SOFTWARETHR A:393 , LEU A:394 , LEU A:395 , GLY A:396 , ASN A:507 , HOH A:1796binding site for residue DMS A 1019
20AE2SOFTWAREASP A:28 , LEU A:29 , ASP A:30 , LYS A:33 , ARG A:171binding site for residue DMS A 1020
21AE3SOFTWAREARG A:14 , ALA A:15 , PRO A:16 , ASP A:17 , HOH A:2601 , HOH A:2779binding site for residue DMS A 1021
22AE4SOFTWAREASP A:216 , ALA A:254 , SER A:273 , HOH A:1749binding site for residue CL A 1022
23AE5SOFTWARELEU A:617 , LEU A:619 , HOH A:1578 , HOH A:1730 , HOH A:1840binding site for residue CL A 1023
24AE6SOFTWAREGLU A:800 , ASP A:801 , HOH A:1870 , HOH A:2464binding site for residue CL A 1024
25AE7SOFTWAREALA A:31 , GLN A:32 , HOH A:1426 , HOH A:2004binding site for residue CL A 1025
26AE8SOFTWAREGLU A:292 , VAL A:670 , HIS A:672 , HOH A:1167 , HOH A:1784binding site for residue GOL A 1026
27AE9SOFTWAREARG A:681 , GLN A:703 , ALA A:707 , ASN A:708 , ASN A:709 , ASP A:712 , HOH A:1333 , HOH A:1909binding site for residue GOL A 1027
28AF1SOFTWAREPHE A:704 , LYS A:738 , TRP A:739 , HOH A:1141 , HOH A:1307 , HOH A:1667 , HOH A:2123binding site for residue GOL A 1028
29AF2SOFTWARETRP A:74 , LYS A:75 , HOH A:1130 , HOH A:1397 , HOH A:1585 , HOH A:1876binding site for residue GOL A 1029
30AF3SOFTWARELEU A:61 , VAL A:62 , TRP A:74 , ARG A:669 , GLU A:671 , HOH A:1155 , HOH A:1397 , HOH A:1973binding site for residue GOL A 1030
31AF4SOFTWAREASP A:58 , LEU A:59 , ILE A:98 , HOH A:1274 , HOH A:1704 , HOH A:1992binding site for residue GOL A 1031
32AF5SOFTWAREASP A:68 , GLU A:69 , ARG A:279 , ASP A:281 , HOH A:1157binding site for residue GOL A 1032
33AF6SOFTWARESER A:112 , ALA A:115 , PHE A:194 , ASP A:216 , ALA A:254 , VAL A:255 , ASP A:256 , HOH A:1158binding site for residue GOL A 1033
34AF7SOFTWAREMET A:368 , PRO A:473 , ASP A:474 , ALA A:476 , HOH A:1122 , HOH A:1328 , HOH A:1359 , HOH A:1888 , HOH A:1919 , HOH A:2018binding site for residue GOL A 1034
35AF8SOFTWAREHIS A:11 , ASP A:12 , ARG A:468 , THR A:469 , LYS A:478 , GLN A:479 , HOH A:1312 , HOH A:1590 , HOH A:1779 , HOH A:1788 , HOH A:1846 , HOH A:2158 , HOH A:2312binding site for residue GOL A 1035
36AF9SOFTWAREARG A:293 , VAL A:324 , ASP A:327 , GLN A:328 , ASN A:344 , GLU A:382 , GOL A:1038 , HOH A:1128 , HOH A:1160 , HOH A:1217 , HOH A:1269 , HOH A:1734 , HOH A:1823 , HOH A:1880binding site for residue GOL A 1036
37AG1SOFTWAREASN A:623 , GLY A:791 , HOH A:1129 , HOH A:1257 , HOH A:1634binding site for residue GOL A 1037
38AG2SOFTWARETYR A:275 , ARG A:293 , MLI A:1012 , GOL A:1036 , HOH A:1114 , HOH A:1160binding site for residue GOL A 1038
39AG3SOFTWAREVAL A:622 , ALA A:638 , THR A:755 , SER A:792 , ASN A:793 , HOH A:1179 , HOH A:1488 , HOH A:1606 , HOH A:1966 , HOH A:2033binding site for residue GOL A 1039

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5MFS)

(-) 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 5MFS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5MFS)

(-) Exons   (0, 0)

(no "Exon" information available for 5MFS)

(-) 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:868
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               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........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
                 5mfs A   3 QQPQAKYRHDYRAPDYQITDIDLTFDLDAQKTVVTAVSQAVRHGASDAPLRLNGEDLKLVSVHINDEPWTAWKEEEGALVISNLPERFTLKIINEISPAANTALEGLYQSGDALCTQCEAEGFRHITYYLDRPDVLARFTTKIIADKIKYPFLLSNGNRVAQGELENGRHWVQWQDPFPKPCYLFALVAGDFDVLRDTFTTRSGREVALELYVDRGNLDRAPWAMTSLKNSMKWDEERFGLEYDLDIYMIVAVDFFNMGAMENKGLNIFNSKYVLARTDTATDKDYLDIERVIGHEYFHNWTGNRVTCRDWFQLSLKEGLTVFRDQEFSSDLGSRAVNRINNVRTMRGLQFAEDASPMAHPIRPDMVIEMNNFYTLTVYEKGAEVIRMIHTLLGEENFQKGMQLYFERHDGSAATCDDFVQAMEDASNVDLSHFRRWYSQSGTPIVTVKDDYNPETEQYTLTISQRTPATPDQAEKQPLHIPFAIELYDNEGKVIPLQKGGHPVNSVLNVTQAEQTFVFDNVYFQPVPALLCEFSAPVKLEYKWSDQQLTFLMRHARNDFSRWDAAQSLLATYIKLNVARHQQGQPLSLPVHVADAFRAVLLDEKIDPALAAEILTLPSVNEMAELFDIIDPIAIAEVREALTRTLATELADELLAIYNANYQSEYRVEHEDIAKRTLRNACLRFLAFGETHLADVLVSKQFHEANNMTDALAALSAAVAAQLPCRDALMQEYDDKWHQNGLVMDKWFILQATSPAANVLETVRGLLQHRSFTMSNPNRIRSLIGAFAGSNPAAFHAEDGSGYLFLVEMLTDLNSRNPQVASRLIEPLIRLKRYDAKRQEKMRAALEQLKGLENLSGDLYEKITKALA 870
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862
   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 5MFS)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5MFS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5MFS)

(-) 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 4q4i 4xmt 4xmu 4xmv 4xmw 4xmx 4xmz 4xn1 4xn2 4xn4 4xn5 4xn7 4xn8 4xn9 4xna 4xnb 4xnd 4xo3 4xo4 4xo5 5mfr 5mft

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