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(-) Description

Title :  CRYSTAL STRUCTURE OF AMINOPEPTIDASE N IN COMPLEX WITH N-CYCLOHEXYL-1, 2-DIAMINOETHYLPHOSPHONIC ACID
 
Authors :  B. Nocek, R. Mulligan, L. Berlicki, S. Vassilious, A. Mucha, A. Joachim
Date :  23 Jun 14  (Deposition) - 24 Sep 14  (Release) - 22 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Alanine Aminopeptidase, Aminopeptidase N, M1 Family Peptidases, N- Cyclohexyl-1, 2-Diaminoethylphosphonic 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 Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    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  (4, 28)

Asymmetric/Biological Unit (4, 28)
No.NameCountTypeFull Name
137E1Ligand/Ion[(1R)-1-AMINO-2-(CYCLOHEXYLAMINO)ETHYL]PHOSPHONIC ACID
2MSE19Mod. Amino AcidSELENOMETHIONINE
3SO47Ligand/IonSULFATE ION
4ZN1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMSE A:103 , GLN A:115 , GLU A:117 , MSE A:256 , ALA A:258 , MSE A:259 , GLU A:260 , HIS A:293 , GLU A:294 , HIS A:297 , GLU A:316 , TYR A:377 , GLN A:818 , ZN A:902 , HOH A:1044 , HOH A:1628BINDING SITE FOR RESIDUE 37E A 901
2AC2SOFTWAREHIS A:293 , HIS A:297 , GLU A:316 , 37E A:901BINDING SITE FOR RESIDUE ZN A 902
3AC3SOFTWAREMSE A:469 , THR A:470 , ASP A:471 , HOH A:1188 , HOH A:1254 , HOH A:1454 , HOH A:1526BINDING SITE FOR RESIDUE SO4 A 903
4AC4SOFTWAREASN A:655 , ARG A:679 , ARG A:683 , HOH A:1525BINDING SITE FOR RESIDUE SO4 A 904
5AC5SOFTWARELEU A:402 , ARG A:406BINDING SITE FOR RESIDUE SO4 A 905
6AC6SOFTWAREARG A:781 , ARG A:822 , HOH A:1441 , HOH A:1470 , HOH A:1521BINDING SITE FOR RESIDUE SO4 A 906
7AC7SOFTWAREARG A:636 , ARG A:755 , HOH A:1012 , HOH A:1587BINDING SITE FOR RESIDUE SO4 A 907
8AC8SOFTWAREARG A:277 , LYS A:736 , HOH A:1351 , HOH A:1379 , HOH A:1654BINDING SITE FOR RESIDUE SO4 A 908
9AC9SOFTWARETHR A:565 , ARG A:568 , ARG A:569 , HOH A:1372 , HOH A:1571 , HOH A:1691BINDING SITE FOR RESIDUE SO4 A 909

(-) SS Bonds  (0, 0)

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

(-) 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 4QPE)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QPE)

(-) 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:867
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               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...hhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee......ee....eeeee.hhh.......hhhhhhhhhhhhhhhhhh.......ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhh...hhhhhhhhh....eeeeeeeee..eeeeeeeee..............eeeeeeee........ee....ee..eeeee...eeeeeee......eeee........eee...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...hhhhhhhhh...hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qpe A   1 mSKTVHYLKDYQTPAYHILKTDLHFDINEPQTVVKSRLTVEPQRVGEPLVLDGSAKLLSVKINGAAADYVLEGETLTIAGVPSERFTVEVETEILPAENKSLmGLYASGGNLFTQCEPEGFRKITFYIDRPDVmSKFTTTIVADKKRYPVLLSNGNKIDGGEFSDGRHWVKWEDPFSKPSYLFALVAGDLAVTEDYFTTmSGRNVKIEFYTTEADKPKVGFAVESLKNAmKWDETRFGLEYDLDIFmVVAVGDFNmGAmENKGLNIFNTKFVLADSRTATDTDFEGIESVVGHEYFHNWTGNRVTCRDWFQLSLKEGLTVFRDQEFSGDRASRAVRRIENIRLLRQHQFPEDAGPTAHPVRPASYEEmNNFYTmTVYEKGAEVVRmYHTLLGEEGFQKGmKLYFQRHDGQAVTCDDFRAAmADANGINLDQFALWYSQAGTPVLEAEGRLKNNIFELTVKQTVPPTPDmTDKQPmmIPVKVGLLNRNGEAVAFDYQGKRATEAVLLLTEAEQTFLLEGVTEAVVPSLLRGFSAPVHLNYPYSDDDLLLLLAHDSDAFTRWEAAQTLYRRAVAANLATLSDGVELPKHEKLLAAVEKVISDDLLDNAFKALLLGVPSEAELWDGAENIDPLRYHQAREALLDTLAVHFLPKWHELNRQAAKQENQSYEYSPEAAGWRTLRNVCRAFVLRADPAHIETVAEKYGEmAQNmTHEWGILSAVNGNESDTRNRLLAQFADKFSDDALVmDKYFALVGSSRRSDTLQQVRTALQHPKFSLENPNKARSLIGSFSRNVPHFHAEDGSGYRFIADKVIEIDRFNPQVAARLVQAFNLCNKLEPHRKNLVKQALQRIRAQEGLSKDVGEIVGKILD 867
                            |       10        20        30        40        50        60        70        80        90       100  |    110       120       130   |   140       150       160       170       180       190       200       210       220       230       240      |250     | 260       270       280       290       300       310       320       330       340       350       360       370   |   380     | 390       400       410       420|      430       440       450       460       470    || 480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700   |   710       720       730       740   |   750       760       770       780       790       800       810       820       830       840       850       860       
                            |                                                                                                   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                                                                                                                       
                            1-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 4QPE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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

(-) Related Entries Specified in the PDB File

2gtq 4pu2 4pvb 4qhp 4qir 4qme