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(-) Description

Title :  CRYSTAL STRUCTURE OF AMINOPEPTIDASE N IN COMPLEX WITH THE PHOSPHINIC DIPEPTIDE ANALOGUE LL-(R,S)-2-(PYRIDIN-3-YL)ETHYLGLYP[CH2]PHE
 
Authors :  B. Nocek, A. Joachimiak, L. Berlicki, S. Vassiliou, A. Mucha
Date :  01 Jun 14  (Deposition) - 24 Sep 14  (Release) - 22 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Alanine Aminopeptidase, Aminopeptidase N, M1 Family Peptidases, 3- {[(R)-1-Amino-3-(Pyridin-3-Yl)Propyl](Hydroxy)Phosphoryl}-(S)-2- Benzylpropanoic Acid, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Vassiliou, E. Weglarz-Tomczak, L. Berlicki, M. Paweczak, B. Nocek R. Mulligan, A. Joachimiak, A. Mucha
Structure-Guided, Single-Point Modifications In The Phosphinic Dipeptide Structure Yield Highly Potent And Selective Inhibitors Of Neutral Aminopeptidases.
J. Med. Chem. V. 57 8140 2014
PubMed-ID: 25192493  |  Reference-DOI: 10.1021/JM501071F

(-) Compounds

Molecule 1 - AMINOPEPTIDASE N
    Chains: A
    EC Number: 3.4.11.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PEPN, NMB1416
    Organism Scientific: NEISSERIA MENINGITIDIS MC58
    Organism Taxid: 122586

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 28)

Asymmetric/Biological Unit (6, 28)
No.NameCountTypeFull Name
13791Ligand/Ion3-{[(R)-1-AMINO-3-(PYRIDIN-3-YL)PROPYL](HYDROXY)PHOSPHORYL}-(S)-2-BENZYLPROPANOIC ACID
2GOL6Ligand/IonGLYCEROL
3IMD1Ligand/IonIMIDAZOLE
4MSE18Mod. Amino AcidSELENOMETHIONINE
5SO41Ligand/IonSULFATE ION
6ZN1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:117 , MSE A:256 , GLY A:257 , ALA A:258 , GLU A:260 , HIS A:293 , GLU A:294 , HIS A:297 , LYS A:315 , GLU A:316 , ASP A:323 , ASN A:369 , TYR A:372 , TYR A:377 , GOL A:906 , ZN A:909BINDING SITE FOR RESIDUE 379 A 901
02AC2SOFTWAREMSE A:469 , THR A:470 , ASP A:471 , HOH A:1242 , HOH A:1770BINDING SITE FOR RESIDUE GOL A 902
03AC3SOFTWAREASN A:655 , ARG A:679 , ARG A:683 , VAL A:697 , LYS A:700 , MSE A:704 , HOH A:1361 , HOH A:1832BINDING SITE FOR RESIDUE GOL A 903
04AC4SOFTWAREPHE A:197 , THR A:198 , LYS A:227 , HOH A:1339 , HOH A:1521BINDING SITE FOR RESIDUE GOL A 904
05AC5SOFTWAREASP A:22 , HIS A:24BINDING SITE FOR RESIDUE IMD A 905
06AC6SOFTWARETYR A:372 , THR A:373 , MSE A:374 , TYR A:377 , 379 A:901BINDING SITE FOR RESIDUE GOL A 906
07AC7SOFTWARETHR A:193 , GLU A:194 , GLU A:625 , LYS A:832 , HOH A:1348 , HOH A:1857BINDING SITE FOR RESIDUE GOL A 907
08AC8SOFTWAREALA A:692 , THR A:696 , ASN A:727 , LEU A:730 , ALA A:731 , TYR A:747 , VAL A:751 , GLN A:762 , HOH A:1011BINDING SITE FOR RESIDUE GOL A 908
09AC9SOFTWAREHIS A:293 , HIS A:297 , GLU A:316 , 379 A:901BINDING SITE FOR RESIDUE ZN A 909
10BC1SOFTWAREARG A:636 , ARG A:755 , HOH A:1134 , HOH A:1720 , HOH A:1727 , HOH A:1810 , HOH A:1890BINDING SITE FOR RESIDUE SO4 A 910

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:29 -Pro A:30
2Glu A:117 -Pro A:118

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QIR)

(-) 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:864
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee.hhh....eeeeeeeeeeee....eeeeeeeeeee......eeee...eeeeeee..ee...eee..eeee.......eeeeeeeeehhhhh....eeeee..eeeee....hhhhh..........eeeeeeeeee.....eeee..eeeeeee....eeeeeeeeeeeehhhhh.eeee..eeeeeeee.....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee......ee....eeeee.hhh.......hhhhhhhhhhhhhhhhhh.......ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhh....hhhhhhhhh....eeeeeeeee..eeeeeeeee..............eeeeeeee.....ee.ee....ee..eeeee...eeeeeee......eeee........eee...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...hhhhhhhhh...hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4qir A   4 TVHYLKDYQTPAYHILKTDLHFDINEPQTVVKSRLTVEPQRVGEPLVLDGSAKLLSVKINGAAADYVLEGETLTIAGVPSERFTVEVETEILPAENKSLmGLYASGGNLFTQCEPEGFRKITFYIDRPDVmSKFTTTIVADKKRYPVLLSNGNKIDGGEFSDGRHWVKWEDPFSKPSYLFALVAGDLAVTEDYFTTmSGRNVKIEFYTTEADKPKVGFAVESLKNAmKWDETRFGLEYDLDIFmVVAVGDFNmGAmENKGLNIFNTKFVLADSRTATDTDFEGIESVVGHEYFHNWTGNRVTCRDWFQLSLKEGLTVFRDQEFSGDRASRAVRRIENIRLLRQHQFPEDAGPTAHPVRPASYEEmNNFYTmTVYEKGAEVVRmYHTLLGEEGFQKGmKLYFQRHDGQAVTCDDFRAAmADANGINLDQFALWYSQAGTPVLEAEGRLKNNIFELTVKQTVPPTPDmTDKQPmmIPVKVGLLNRNGEAVAFDYQGKRATEAVLLLTEAEQTFLLEGVTEAVVPSLLRGFSAPVHLNYPYSDDDLLLLLAHDSDAFTRWEAAQTLYRRAVAANLATLSDGVELPKHEKLLAAVEKVISDDLLDNAFKALLLGVPSEAELWDGAENIDPLRYHQAREALLDTLAVHFLPKWHELNRQAAKQENQSYEYSPEAAGWRTLRNVCRAFVLRADPAHIETVAEKYGEmAQNmTHEWGILSAVNGNESDTRNRLLAQFADKFSDDALVmDKYFALVGSSRRSDTLQQVRTALQHPKFSLENPNKARSLIGSFSRNVPHFHAEDGSGYRFIADKVIEIDRFNPQVAARLVQAFNLCNKLEPHRKNLVKQALQRIRAQEGLSKDVGEIVGKILD 867
                                    13        23        33        43        53        63        73        83        93       103       113       123       133|      143       153       163       173       183       193      |203       213       223      |233       243   |   253  |  | 263       273       283       293       303       313       323       333       343       353       363    |  373|      383  |    393      |403       413       423       433       443       453       463     | 473 ||    483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703|   |  713       723       733       743|      753       763       773       783       793       803       813       823       833       843       853       863    
                                                                                                                             103-MSE                        134-MSE                                                           200-MSE                       230-MSE          247-MSE  256-MSE                                                                                                         368-MSE |         386-MSE       400-MSE              421-MSE                                         469-MSE ||                                                                                                                                                                                                                                 704-MSE                                 744-MSE                                                                                                                       
                                                                                                                                                                                                                                                                                         259-MSE                                                                                                            374-MSE                                                                                              475-MSE                                                                                                                                                                                                                                  708-MSE                                                                                                                                                           
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  476-MSE
   Legend:   → Mismatch (orange background)
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  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 4QIR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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        Q9JYV4_NEIMB | Q9JYV4: 2gtq 4pu2 4pvb 4pw4 4qhp 4qme 4qpe 4quo 5dyf

(-) Related Entries Specified in the PDB File

4pu2 4pvb 4pw4 4qhp 4qme 4qpe