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(-) Description

Title :  CRYSTAL STRUCTURE OF AMINOPEPTIDASE N IN COMPLEX WITH THE PHOSPHINIC DIPEPTIDE ANALOGUE LL-(R,S)-HPHEP[CH2]PHE
 
Authors :  B. Nocek, S. Vassilious, R. Mulligan, L. Berlicki, A. Mucha, A. Joachim
Date :  16 Jun 14  (Deposition) - 01 Oct 14  (Release) - 22 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Apn, Alanine Aminopeptidase, M1 Peptidase, 3-{[(R)-1-Amino-3- Phenylpropyl](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, 31)

Asymmetric/Biological Unit (6, 31)
No.NameCountTypeFull Name
137B1Ligand/Ion(2S)-3-[(S)-[(1R)-1-AMINO-3-PHENYLPROPYL](HYDROXY)PHOSPHORYL]-2-BENZYLPROPANOIC ACID
2GOL2Ligand/IonGLYCEROL
3IMD2Ligand/IonIMIDAZOLE
4MSE18Mod. Amino AcidSELENOMETHIONINE
5SO47Ligand/IonSULFATE ION
6ZN1Ligand/IonZINC ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:115 , GLU A:117 , MSE A:256 , GLY A:257 , ALA A:258 , GLU A:260 , VAL A:290 , HIS A:293 , GLU A:294 , HIS A:297 , LYS A:315 , GLU A:316 , ASP A:323 , TYR A:377 , ZN A:908 , GOL A:910 , HOH A:1935BINDING SITE FOR RESIDUE 37B A 901
02AC2SOFTWAREHIS A:293 , HIS A:297 , GLU A:316 , 37B A:901BINDING SITE FOR RESIDUE ZN A 908
03AC3SOFTWARETYR A:196 , PHE A:197 , THR A:198 , LYS A:227 , HOH A:1516 , HOH A:1774BINDING SITE FOR RESIDUE GOL A 909
04AC4SOFTWARETYR A:372 , THR A:373 , TYR A:377 , GLU A:378 , 37B A:901BINDING SITE FOR RESIDUE GOL A 910
05AC5SOFTWAREARG A:203 , LEU A:243 , ASP A:244BINDING SITE FOR RESIDUE IMD A 911
06AC6SOFTWAREASP A:22 , HIS A:24BINDING SITE FOR RESIDUE IMD A 912
07AC7SOFTWAREARG A:636 , ARG A:755 , HOH A:1137 , HOH A:1385 , HOH A:1542 , HOH A:1632 , HOH A:2077BINDING SITE FOR RESIDUE SO4 A 913
08AC8SOFTWAREMSE A:469 , THR A:470 , ASP A:471 , HOH A:1294 , HOH A:1954 , HOH A:1970 , HOH A:2034 , HOH A:2106 , HOH A:2109BINDING SITE FOR RESIDUE SO4 A 914
09AC9SOFTWAREARG A:330 , HOH A:1629 , HOH A:1846BINDING SITE FOR RESIDUE SO4 A 915
10BC1SOFTWAREARG A:406BINDING SITE FOR RESIDUE SO4 A 916
11BC2SOFTWARETHR A:565 , ARG A:568 , ARG A:569 , HOH A:1563 , HOH A:1980 , HOH A:2154BINDING SITE FOR RESIDUE SO4 A 917
12BC3SOFTWAREALA A:191 , VAL A:192 , ASN A:831 , LYS A:838 , LYS A:842 , HOH A:1526 , HOH A:2090BINDING SITE FOR RESIDUE SO4 A 918
13BC4SOFTWAREALA A:331 , SER A:332 , HOH A:1033 , HOH A:1612 , HOH A:1736BINDING SITE FOR RESIDUE SO4 A 919

(-) SS Bonds  (0, 0)

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

(-) 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 4QME)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QME)

(-) 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:866
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               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...........eeeeeeeee.....eeee..eeeeeee....eeeeeee.....hhhhh.eeee..eeeeeeee.....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee......ee....eeeee.hhh.......hhhhhhhhhhhhhhhhhh.......ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhh...hhhhhhhhh....eeeeeeeee..eeeeeeeee..............eeeeeeee.....ee.eee..eee..eeeee...eeeeeee......eeee........eee...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...hhhhhhhhh...hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qme A   2 SKTVHYLKDYQTPAYHILKTDLHFDINEPQTVVKSRLTVEPQRVGEPLVLDGSAKLLSVKINGAAADYVLEGETLTIAGVPSERFTVEVETEILPAENKSLmGLYASGGNLFTQCEPEGFRKITFYIDRPDVmSKFTTTIVADKKRYPVLLSNGNKIDGGEFSDGRHWVKWEDPFSKPSYLFALVAGDLAVTEDYFTTmSGRNVKIEFYTTEADKPKVGFAVESLKNAmKWDETRFGLEYDLDIFmVVAVGDFNmGAmENKGLNIFNTKFVLADSRTATDTDFEGIESVVGHEYFHNWTGNRVTCRDWFQLSLKEGLTVFRDQEFSGDRASRAVRRIENIRLLRQHQFPEDAGPTAHPVRPASYEEmNNFYTmTVYEKGAEVVRmYHTLLGEEGFQKGmKLYFQRHDGQAVTCDDFRAAmADANGINLDQFALWYSQAGTPVLEAEGRLKNNIFELTVKQTVPPTPDmTDKQPmmIPVKVGLLNRNGEAVAFDYQGKRATEAVLLLTEAEQTFLLEGVTEAVVPSLLRGFSAPVHLNYPYSDDDLLLLLAHDSDAFTRWEAAQTLYRRAVAANLATLSDGVELPKHEKLLAAVEKVISDDLLDNAFKALLLGVPSEAELWDGAENIDPLRYHQAREALLDTLAVHFLPKWHELNRQAAKQENQSYEYSPEAAGWRTLRNVCRAFVLRADPAHIETVAEKYGEmAQNmTHEWGILSAVNGNESDTRNRLLAQFADKFSDDALVmDKYFALVGSSRRSDTLQQVRTALQHPKFSLENPNKARSLIGSFSRNVPHFHAEDGSGYRFIADKVIEIDRFNPQVAARLVQAFNLCNKLEPHRKNLVKQALQRIRAQEGLSKDVGEIVGKILD 867
                                    11        21        31        41        51        61        71        81        91       101 |     111       121       131  |    141       151       161       171       181       191       201       211       221       231       241     | 251    |  261       271       281       291       301       311       321       331       341       351       361      |371  |    381    |  391       401       411       421       431       441       451       461       471   ||  481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701  |   |711       721       731       741  |    751       761       771       781       791       801       811       821       831       841       851       861      
                                                                                                                               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)
  - → 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 4QME)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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        Q9JYV4_NEIMB | Q9JYV4: 2gtq 4pu2 4pvb 4pw4 4qhp 4qir 4qpe 4quo 5dyf

(-) Related Entries Specified in the PDB File

4qir 4qpe