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(-) Description

Title :  CRYSTAL STRUCTURE OF AMINOPEPTIDASE N IN COMPLEX WITH THE PHOSPHINIC DIPEPTIDE ANALOGUE LL-(R,S)-HPHEP[CH2]PHE(4-CH2NH2)
 
Authors :  B. Nocek, A. Joachimiak
Date :  28 May 14  (Deposition) - 24 Sep 14  (Release) - 22 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Zn-Dependent, Apn, (S)-2-[4-(Aminomethyl)Benzyl]-3-[(R)-1-Amino-3- Phenylpropyl(Hydroxy)Phosphoryl]Propanoic Acid, Hydrolase-Hydrolase Inhibitor Complex (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
    Organism Taxid: 487

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 36)

Asymmetric/Biological Unit (7, 36)
No.NameCountTypeFull Name
132Q1Ligand/Ion(2S)-2-[4-(AMINOMETHYL)BENZYL]-3-[(R)-[(1R)-1-AMINO-3-PHENYLPROPYL](HYDROXY)PHOSPHORYL]PROPANOIC ACID
232R1Ligand/Ion(2R)-2-[4-(AMINOMETHYL)BENZYL]-3-[(R)-[(1R)-1-AMINO-3-PHENYLPROPYL](HYDROXY)PHOSPHORYL]PROPANOIC ACID
3GOL4Ligand/IonGLYCEROL
4IMD1Ligand/IonIMIDAZOLE
5MSE18Mod. Amino AcidSELENOMETHIONINE
6SO410Ligand/IonSULFATE ION
7ZN1Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
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 , GLU A:378 , ZN A:908 , HOH A:1489BINDING SITE FOR RESIDUE 32Q A 901
02AC2SOFTWAREASN A:156 , PRO A:175 , PHE A:176 , ARG A:203 , TYR A:241 , ASP A:242 , LEU A:243 , ASP A:244 , GOL A:907 , HOH A:1063 , HOH A:1234 , HOH A:1613 , HOH A:1635 , HOH A:1766BINDING SITE FOR RESIDUE 32R A 902
03AC3SOFTWAREHIS A:24 , LYS A:35 , ARG A:37BINDING SITE FOR RESIDUE IMD A 903
04AC4SOFTWARETYR A:196 , PHE A:197 , THR A:198 , LYS A:227 , HOH A:1760 , HOH A:1834BINDING SITE FOR RESIDUE GOL A 904
05AC5SOFTWAREPRO A:585 , LYS A:586 , HIS A:587 , GLU A:588 , LYS A:589 , HOH A:1687 , HOH A:1953BINDING SITE FOR RESIDUE GOL A 905
06AC6SOFTWAREALA 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:1061BINDING SITE FOR RESIDUE GOL A 906
07AC7SOFTWAREARG A:203 , 32R A:902BINDING SITE FOR RESIDUE GOL A 907
08AC8SOFTWAREHIS A:293 , HIS A:297 , GLU A:316 , 32Q A:901BINDING SITE FOR RESIDUE ZN A 908
09AC9SOFTWAREMSE A:469 , THR A:470 , ASP A:471 , HOH A:1101 , HOH A:1179 , HOH A:1397 , HOH A:1462 , HOH A:1568BINDING SITE FOR RESIDUE SO4 A 909
10BC1SOFTWAREASN A:655 , ARG A:679 , ARG A:683 , LYS A:700 , MSE A:704 , HOH A:1558 , HOH A:1804BINDING SITE FOR RESIDUE SO4 A 910
11BC2SOFTWAREARG A:406BINDING SITE FOR RESIDUE SO4 A 911
12BC3SOFTWAREARG A:636 , ARG A:755 , HOH A:1053 , HOH A:1270 , HOH A:1515 , HOH A:1608 , HOH A:1611 , HOH A:1675 , HOH A:1832BINDING SITE FOR RESIDUE SO4 A 912
13BC4SOFTWAREARG A:277 , HOH A:1688BINDING SITE FOR RESIDUE SO4 A 913
14BC5SOFTWARETHR A:565 , ARG A:568 , ARG A:569 , HOH A:1298 , HOH A:1664BINDING SITE FOR RESIDUE SO4 A 914
15BC6SOFTWAREARG A:330 , HOH A:1480 , HOH A:1732BINDING SITE FOR RESIDUE SO4 A 915
16BC7SOFTWAREARG A:499 , HOH A:1466BINDING SITE FOR RESIDUE SO4 A 916
17BC8SOFTWAREGLN A:664 , TYR A:666 , ARG A:679 , MSE A:704 , HOH A:1471BINDING SITE FOR RESIDUE SO4 A 917
18BC9SOFTWAREALA A:191 , VAL A:192 , ASN A:831 , LYS A:838 , LYS A:842 , HOH A:1380 , HOH A:1654BINDING SITE FOR RESIDUE SO4 A 918

(-) SS Bonds  (0, 0)

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

(-) 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 4QHP)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QHP)

(-) 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.........eeeeeeeeeee.....eeee..eeeeeee....eeeeeee....ee.hhh.eeee..eeeeeeee.....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee......ee....eeeee.hhh.......hhhhhhhhhhhhhhhhhh.......ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhh...hhhhhhhhhh....eeeeeeeee..eeeeeeeee..............eeeeeeee........ee....ee..eeeee...eeeeeee......eeee........eee...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh......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
                 4qhp 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 4QHP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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  3.4.11.2
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        Q9JYV4_NEIMB | Q9JYV4: 2gtq 4pu2 4pvb 4pw4 4qir 4qme 4qpe 4quo 5dyf

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