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(-) Description

Title :  CRYSTAL STRUCTURE OF RAT NEUROLYSIN WITH BOUND PYRAZOLIDIN INHIBITOR
 
Authors :  D. W. Rodgers, C. S. Hines
Date :  03 Jul 12  (Deposition) - 13 Nov 13  (Release) - 14 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  P,Q
Biol. Unit 1:  P  (1x)
Biol. Unit 2:  Q  (1x)
Keywords :  Hydrolase, Endopeptidase, Zinc Metallopeptidase, Neuropeptidase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. S. Hines, K. Ray, J. J. Schmidt, F. Xiong, R. W. Feenstra, M. Pras-Raves, J. P. De Moes, J. H. Lange, M. Melikishvili, M. G. Fried P. Mortenson, M. Charlton, Y. Patel, S. M. Courtney, C. G. Kruse, D. W. Rodgers
Allosteric Inhibition Of The Neuropeptidase Neurolysin.
J. Biol. Chem. V. 289 35605 2014
PubMed-ID: 25378390  |  Reference-DOI: 10.1074/JBC.M114.620930

(-) Compounds

Molecule 1 - NEUROLYSIN, MITOCHONDRIAL
    Chains: P, Q
    EC Number: 3.4.24.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD/HIS C
    Expression System Strain: TOP 10
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NLN
    Mutation: YES
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: MICROSOMAL ENDOPEPTIDASE, MEP, MITOCHONDRIAL OLIGOPEPTIDASE M, NEUROTENSIN ENDOPEPTIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : PQ
Biological Unit 1 (1x): P 
Biological Unit 2 (1x):  Q

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
10W22Ligand/Ion1-{(2S)-1-[(3R)-3-(2-CHLOROPHENYL)-2-(2-FLUOROPHENYL)PYRAZOLIDIN-1-YL]-1-OXOPROPAN-2-YL}-3-[(1R,3S,5R,7R)-TRICYCLO[3.3.1.1~3,7~]DEC-2-YL]UREA
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
10W21Ligand/Ion1-{(2S)-1-[(3R)-3-(2-CHLOROPHENYL)-2-(2-FLUOROPHENYL)PYRAZOLIDIN-1-YL]-1-OXOPROPAN-2-YL}-3-[(1R,3S,5R,7R)-TRICYCLO[3.3.1.1~3,7~]DEC-2-YL]UREA
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
10W21Ligand/Ion1-{(2S)-1-[(3R)-3-(2-CHLOROPHENYL)-2-(2-FLUOROPHENYL)PYRAZOLIDIN-1-YL]-1-OXOPROPAN-2-YL}-3-[(1R,3S,5R,7R)-TRICYCLO[3.3.1.1~3,7~]DEC-2-YL]UREA
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR P:45 , TYR P:49 , LEU P:69 , ILE P:72 , GLU P:73 , TYR P:76 , ARG P:80 , ASP P:110 , MET P:113 , ILE P:123 , SER P:146 , ARG P:491 , HOH P:837 , HOH P:838 , HOH P:927BINDING SITE FOR RESIDUE 0W2 P 701
2AC2SOFTWAREHIS P:474 , GLU P:475 , HIS P:478 , GLU P:503 , HOH P:843BINDING SITE FOR RESIDUE ZN P 702
3AC3SOFTWARETHR Q:45 , TYR Q:49 , LEU Q:69 , ILE Q:72 , GLU Q:73 , TYR Q:76 , ARG Q:80 , ASP Q:110 , MET Q:113 , ARG Q:116 , ILE Q:123 , SER Q:146 , ARG Q:491 , HOH Q:928 , HOH Q:929 , HOH Q:930BINDING SITE FOR RESIDUE 0W2 Q 701
4AC4SOFTWAREHIS Q:474 , GLU Q:475 , HIS Q:478 , GLU Q:503 , HOH Q:836BINDING SITE FOR RESIDUE ZN Q 702

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4FXY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FXY)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FXY)

(-) Sequences/Alignments

Asymmetric 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 P from PDB  Type:PROTEIN  Length:664
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4fxyp_ P: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh...eeee........hhhhhhh.ee.....eeee.hhhhhhhhhhhh.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhheeeee...........eeeeeee.....eeeeeeee...........eeeeee............eeeeee..............hhhhhhhhhhhhhhhhhhhhh...hhhhh.........hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh.........hhhhh............hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.......hhhhhhhh.......hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fxy P  15 SSYTAAGRNVLRWDLSPEQIKTRTEQLIAQTKQVYDTVGTIALKEVTYENCLQVLADIEVTYIVERTMLDFPQHVSSDREVRAASTEADKKLSRFDIEMSMREDVFQRIVHLQETCDLEKIKPEARRYLEKSIKMGKRNGLHLSEAIRNEIKSMKKRMSELCIDFNKNLNEDDTSLVFSKAELGALPDDFIDSLEKTDEDKYKVTLKYPHYFPVMKKCCVPETRRKMEMAFHTRCKQENTAILQQLLPLRAQVAKLLGYNTHADFVLELNTAKSTSRVAAFLDDLSQKLKPLGEAEREFILSLKKKECEERGFEYDGKINAWDLHYYMTQTEELKYSVDQESLKEYFPIEVVTEGLLSIYQELLGLSFEQVPDAHVWNKSVSLYTVKDKATGEVLGQFYLDLYPREGKYNHAACFGLQPGCLLPDGSRMMSVAALVVNFSQPVAGRPSLLRHDEVRTYFHEFGHVMHQICAQTDFARFSGTNVETDFVEVPSQMLENWVWDVDSLRKLSKHYKDGHPITDELLEKLVASRLVNTGLLTLRQIVLSKVDQSLHTNATLDAASEYAKYCTEILGVAATPGTNMPATFGHLAGGYDGQYYGYLWSEVFSMDMFHSCFKKEGIMNPEVGMKYRNLILKPGGSLDGMDMLQNFLQREPNQKAFLMSRGL 678
                                    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    


Chain Q from PDB  Type:PROTEIN  Length:664
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4fxyq_ Q: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh...eeee........hhhhhhh.ee.....eeee.hhhhhhhhhhhh.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhheeeee...........eeeeeee.....eeeeeeee...........eeeeee............eeeeee..............hhhhhhhhhhhhhhhhhhhhh...hhhhh.........hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh.........hhhhh............hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.......hhhhhhhh.......hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fxy Q  15 SSYTAAGRNVLRWDLSPEQIKTRTEQLIAQTKQVYDTVGTIALKEVTYENCLQVLADIEVTYIVERTMLDFPQHVSSDREVRAASTEADKKLSRFDIEMSMREDVFQRIVHLQETCDLEKIKPEARRYLEKSIKMGKRNGLHLSEAIRNEIKSMKKRMSELCIDFNKNLNEDDTSLVFSKAELGALPDDFIDSLEKTDEDKYKVTLKYPHYFPVMKKCCVPETRRKMEMAFHTRCKQENTAILQQLLPLRAQVAKLLGYNTHADFVLELNTAKSTSRVAAFLDDLSQKLKPLGEAEREFILSLKKKECEERGFEYDGKINAWDLHYYMTQTEELKYSVDQESLKEYFPIEVVTEGLLSIYQELLGLSFEQVPDAHVWNKSVSLYTVKDKATGEVLGQFYLDLYPREGKYNHAACFGLQPGCLLPDGSRMMSVAALVVNFSQPVAGRPSLLRHDEVRTYFHEFGHVMHQICAQTDFARFSGTNVETDFVEVPSQMLENWVWDVDSLRKLSKHYKDGHPITDELLEKLVASRLVNTGLLTLRQIVLSKVDQSLHTNATLDAASEYAKYCTEILGVAATPGTNMPATFGHLAGGYDGQYYGYLWSEVFSMDMFHSCFKKEGIMNPEVGMKYRNLILKPGGSLDGMDMLQNFLQREPNQKAFLMSRGL 678
                                    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
   Legend:   → Mismatch (orange background)
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    → 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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

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  4fxy
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 Related Entries

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

UniProtKB/Swiss-Prot
        NEUL_RAT | P42676: 1i1i 2o3e

(-) Related Entries Specified in the PDB File

1i1i CRYSTAL STRUCTURE OF NEUROLYSIN WITHOUT BOUND LIGAND
2o3e CRYSTAL STRUCTURE OF ENGINEERED NEUROLYSIN WITH ALTERED SPECIFICITY