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(-) Description

Title :  THE CRYSTAL STRUCTURE OF E. COLI AMINOPEPTIDASE N IN COMPLEX WITH 7-AMINO-1-BROMO-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 :  1.59
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, 25)

Asymmetric/Biological Unit (7, 25)
No.NameCountTypeFull Name
17MF1Ligand/Ion[(7~{S})-1-BROMANYL-6,6-BIS(OXIDANYL)-4-PHENYL-5,7,8,9-TETRAHYDROBENZO[7]ANNULEN-7-YL]AZANIUM
2CL2Ligand/IonCHLORIDE ION
3DMS2Ligand/IonDIMETHYL SULFOXIDE
4GOL8Ligand/IonGLYCEROL
5MLI5Ligand/IonMALONATE ION
6NA6Ligand/IonSODIUM ION
7ZN1Ligand/IonZINC ION

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:297 , HIS A:301 , GLU A:320 , 7MF 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:376 , TYR A:381 , ARG A:825 , ZN A:1001 , MLI A:1021binding site for residue 7MF A 1002
03AC3SOFTWARESER A:332 , ASP A:333 , GLY A:335 , HOH A:2067 , HOH A:2278 , HOH A:2357binding site for residue NA A 1003
04AC4SOFTWAREHIS A:771 , PHE A:774 , HOH A:1493 , HOH A:1551 , HOH A:2270 , HOH A:2325binding site for residue NA A 1004
05AC5SOFTWARESER A:508 , HOH A:2008 , HOH A:2172 , HOH A:2223 , HOH A:2410 , HOH A:2933binding site for residue NA A 1005
06AC6SOFTWAREASP A:452 , HOH A:1268 , HOH A:1379 , HOH A:2336 , HOH A:2344 , HOH A:2842binding site for residue NA A 1006
07AC7SOFTWAREGLU A:123 , GLU A:371 , HOH A:1153 , HOH A:1298 , HOH A:1682 , HOH A:1693 , HOH A:2373binding site for residue NA A 1007
08AC8SOFTWAREASN A:399 , SER A:429 , HOH A:1595 , HOH A:1658 , HOH A:2035 , HOH A:2246binding site for residue NA A 1008
09AC9SOFTWARELEU A:61 , VAL A:62 , TRP A:74 , ARG A:669 , GLU A:671 , HOH A:1126 , HOH A:1871 , HOH A:2079binding site for residue GOL A 1009
10AD1SOFTWAREASN A:623 , GLY A:791 , HOH A:1113 , HOH A:1253 , HOH A:1625binding site for residue GOL A 1010
11AD2SOFTWAREPHE A:704 , HIS A:705 , ALA A:707 , TYR A:735 , LYS A:738 , TRP A:739 , HOH A:1161 , HOH A:1559 , HOH A:1832binding site for residue GOL A 1011
12AD3SOFTWARETRP A:74 , LYS A:75 , HOH A:1196 , HOH A:1484 , HOH A:1871 , HOH A:2073binding site for residue GOL A 1012
13AD4SOFTWAREMET A:368 , PRO A:473 , ASP A:474 , ALA A:476 , HOH A:1110 , HOH A:1357 , HOH A:1629 , HOH A:1755 , HOH A:1758 , HOH A:2084 , HOH A:2105binding site for residue GOL A 1013
14AD5SOFTWAREASP A:58 , LEU A:59 , GLU A:97 , ILE A:98 , SER A:99 , HOH A:1395 , HOH A:2110binding site for residue GOL A 1014
15AD6SOFTWAREHIS A:11 , ASP A:12 , ARG A:14 , ARG A:468 , THR A:469 , LYS A:478 , GLN A:479 , HOH A:1179 , HOH A:1191 , HOH A:1805 , HOH A:1875 , HOH A:2322 , HOH A:2822binding site for residue GOL A 1015
16AD7SOFTWARELYS A:541 , GLU A:627 , PHE A:629 , ASP A:630 , ARG A:835 , HOH A:1261 , HOH A:1276 , HOH A:2128binding site for residue GOL A 1016
17AD8SOFTWARETHR A:393 , LEU A:394 , LEU A:395 , GLY A:396 , ASN A:507 , HOH A:1782binding site for residue DMS A 1017
18AD9SOFTWARETHR A:393 , GLU A:535 , HOH A:1157binding site for residue DMS A 1018
19AE1SOFTWAREASP A:216 , ASN A:219 , ALA A:254 , SER A:273 , HOH A:1698binding site for residue CL A 1019
20AE2SOFTWAREALA A:31 , GLN A:32 , HOH A:1490 , HOH A:2131binding site for residue CL A 1020
21AE3SOFTWARETYR A:376 , THR A:377 , LEU A:378 , TYR A:381 , GLU A:382 , ARG A:825 , 7MF A:1002 , HOH A:1115 , HOH A:1224binding site for residue MLI A 1021
22AE4SOFTWAREGLY A:396 , GLU A:397 , GLU A:398 , HOH A:1119 , HOH A:1204 , HOH A:1246 , HOH A:1591 , HOH A:1763 , HOH A:1996 , HOH A:2136 , HOH A:2576binding site for residue MLI A 1022
23AE5SOFTWAREALA A:531 , LEU A:532 , TRP A:546 , LEU A:551 , LEU A:554 , ASP A:566 , ALA A:567 , SER A:570 , HOH A:1105 , HOH A:1714binding site for residue MLI A 1023
24AE6SOFTWARELYS A:8 , GLU A:123 , TRP A:313 , PHE A:314 , VAL A:369 , MET A:372 , HOH A:1153 , HOH A:1181 , HOH A:1271 , HOH A:1600binding site for residue MLI A 1024
25AE7SOFTWAREASP A:28 , LEU A:29 , ASP A:30 , LYS A:33 , ARG A:171 , HOH A:1205 , HOH A:2131binding site for residue MLI A 1025

(-) SS Bonds  (0, 0)

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

(-) 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 5MFT)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5MFT)

(-) 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
                 5mft 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 5MFT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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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 5mfs

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