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(-) Description

Title :  THE CRYSTAL STRUCTURE OF E. COLI AMINOPEPTIDASE N IN COMPLEX WITH 7-AMINO-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 :  1.40
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 BL21(DE3)
    Expression System Taxid: 469008
    Gene: PEPN, B0932, JW0915
    Organism Scientific: ESCHERICHIA COLI (STRAIN K12)
    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, 29)

Asymmetric/Biological Unit (7, 29)
No.NameCountTypeFull Name
17MK1Ligand/Ion[(7~{S})-6,6-BIS(OXIDANYL)-5,7,8,9-TETRAHYDROBENZO[7]ANNULEN-7-YL]AZANIUM
2CL3Ligand/IonCHLORIDE ION
3DMS2Ligand/IonDIMETHYL SULFOXIDE
4GOL10Ligand/IonGLYCEROL
5MLI4Ligand/IonMALONATE ION
6NA8Ligand/IonSODIUM ION
7ZN1Ligand/IonZINC ION

(-) Sites  (29, 29)

Asymmetric Unit (29, 29)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:297 , HIS A:301 , GLU A:320 , 7MK A:1002 , GOL A:1011binding site for residue ZN A 1001
02AC2SOFTWAREGLU A:121 , MET A:260 , ALA A:262 , GLU A:264 , HIS A:297 , GLU A:298 , HIS A:301 , LYS A:319 , GLU A:320 , TYR A:381 , ZN A:1001 , GOL A:1011 , MLI A:1021 , MLI A:1022 , HOH A:1358 , HOH A:1672 , HOH A:2243 , HOH A:2536binding site for residue 7MK A 1002
03AC3SOFTWAREASN A:623 , GLY A:791 , ARG A:832 , HOH A:1119 , HOH A:1229 , HOH A:1232binding site for residue GOL A 1003
04AC4SOFTWAREGLU A:292 , VAL A:670 , HIS A:672 , GOL A:1009 , HOH A:1387 , HOH A:1869 , HOH A:2341 , HOH A:2650binding site for residue GOL A 1004
05AC5SOFTWAREPHE A:704 , ALA A:707 , LYS A:738 , TRP A:739 , HOH A:1120 , HOH A:1267 , HOH A:1780binding site for residue GOL A 1005
06AC6SOFTWARELEU A:61 , VAL A:62 , ARG A:669 , GLU A:671 , HOH A:1239 , HOH A:1310 , HOH A:2074 , HOH A:2108 , HOH A:2130 , HOH A:2789binding site for residue GOL A 1006
07AC7SOFTWAREASP A:58 , LEU A:59 , GLU A:97 , ILE A:98 , SER A:99 , HOH A:1492 , HOH A:1734 , HOH A:1938 , HOH A:2081 , HOH A:2216binding site for residue GOL A 1007
08AC8SOFTWAREHIS A:11 , ASP A:12 , ARG A:14 , ARG A:468 , THR A:469 , LYS A:478 , GLN A:479 , HOH A:1138 , HOH A:1401 , HOH A:1825 , HOH A:1845 , HOH A:2289 , HOH A:2761binding site for residue GOL A 1008
09AC9SOFTWARETRP A:74 , GLU A:671 , GOL A:1004 , HOH A:1187 , HOH A:1902 , HOH A:2789binding site for residue GOL A 1009
10AD1SOFTWAREMET A:368 , PRO A:473 , ASP A:474 , ALA A:476 , HOH A:1126 , HOH A:1279 , HOH A:1395 , HOH A:1534 , HOH A:1587 , HOH A:1913binding site for residue GOL A 1010
11AD2SOFTWAREGLU A:121 , ALA A:262 , GLU A:264 , HIS A:297 , GLU A:298 , HIS A:301 , LYS A:319 , GLU A:320 , TYR A:381 , ZN A:1001 , 7MK A:1002 , MLI A:1021 , HOH A:1358 , HOH A:1672 , HOH A:2536binding site for residue GOL A 1011
12AD3SOFTWARELYS A:541 , GLU A:627 , PHE A:629 , ASP A:630 , ARG A:835 , HOH A:1673 , HOH A:2324binding site for residue GOL A 1012
13AD4SOFTWARESER A:332 , ASP A:333 , GLY A:335 , HOH A:1970 , HOH A:2209 , HOH A:2332binding site for residue NA A 1013
14AD5SOFTWAREHIS A:771 , PHE A:774 , HOH A:1400 , HOH A:1633 , HOH A:2196 , HOH A:2222binding site for residue NA A 1014
15AD6SOFTWARESER A:508 , HOH A:1924 , HOH A:1999 , HOH A:2163 , HOH A:2359 , HOH A:2835binding site for residue NA A 1015
16AD7SOFTWAREASP A:452 , HOH A:1149 , HOH A:1263 , HOH A:2265 , HOH A:2283 , HOH A:2692binding site for residue NA A 1016
17AD8SOFTWAREGLU A:123 , GLU A:371 , HOH A:1159 , HOH A:1273 , HOH A:1418 , HOH A:1597 , HOH A:2317binding site for residue NA A 1017
18AD9SOFTWAREASN A:67 , THR A:91 , HOH A:2246 , HOH A:2394 , HOH A:2409binding site for residue NA A 1018
19AE1SOFTWAREASP A:452 , TYR A:544 , HOH A:1535 , HOH A:2340 , HOH A:2504binding site for residue NA A 1019
20AE2SOFTWAREMET A:260 , ASN A:373 , GLN A:821 , HOH A:1591 , HOH A:1701 , HOH A:2146binding site for residue NA A 1020
21AE3SOFTWARETYR A:275 , ARG A:293 , HIS A:297 , GLU A:298 , 7MK A:1002 , GOL A:1011 , MLI A:1022 , HOH A:1165 , HOH A:1669 , HOH A:2536binding site for residue MLI A 1021
22AE4SOFTWARETYR A:376 , THR A:377 , LEU A:378 , TYR A:381 , GLU A:382 , ARG A:825 , 7MK A:1002 , MLI A:1021 , HOH A:1165binding site for residue MLI A 1022
23AE5SOFTWARELYS A:8 , GLU A:123 , TRP A:313 , PHE A:314 , VAL A:369 , MET A:372 , HOH A:1136 , HOH A:1159 , HOH A:1193 , HOH A:1929binding site for residue MLI A 1023
24AE6SOFTWAREASP A:28 , LEU A:29 , ASP A:30 , LYS A:33 , VAL A:35 , ARG A:171 , HOH A:1116 , HOH A:1178 , HOH A:2039binding site for residue MLI A 1024
25AE7SOFTWARETHR A:393 , LEU A:394 , LEU A:395 , GLY A:396 , ASN A:507 , HOH A:1859binding site for residue DMS A 1025
26AE8SOFTWARETHR A:393 , GLU A:535 , HOH A:1166 , HOH A:2131binding site for residue DMS A 1026
27AE9SOFTWAREASP A:216 , ALA A:254 , SER A:273 , HOH A:1661binding site for residue CL A 1027
28AF1SOFTWAREASN A:560 , ASP A:561 , HOH A:2466binding site for residue CL A 1028
29AF2SOFTWAREALA A:31 , GLN A:32 , HOH A:2039binding site for residue CL A 1029

(-) SS Bonds  (0, 0)

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

(-) 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 5MFR)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5MFR)

(-) 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
                 5mfr 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 5MFR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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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 4xo3 4xo4 4xo5 5mfs 5mft

(-) Related Entries Specified in the PDB File

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