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(-) Description

Title :  THE CRYSTAL STRUCTURE OF AMINOPEPTIDASE N IN COMPLEX WITH N-BENZYL-1, 2-DIAMINOETHYLPHOSPHONIC ACID
 
Authors :  B. Nocek, A. Joachimiak, S. Vassiliou, L. Berlicki, A. Mucha, Midwest For Structural Genomics (Mcsg)
Date :  24 Sep 15  (Deposition) - 25 Nov 15  (Release) - 25 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Aminopeptidasen, Inhibitor Complex, N-Benzyl-1, 2- Diaminoethylphosphonic Acid, Hydrolase-Hydrolase Inhibitor Complex, Structural Genomics, Psi-Biology, Midwest Center For Structural Genomics, Mcsg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Nocek, A. Joachimiak, S. Vassiliou, L. Berlicki, A. Mucha, Midwest Center For Structural Genomics (Mcsg)
The Crystal Structure Of Aminopeptidase N In Complex With N-Benzyl-1, 2-Diaminoethylphosphonic Acid
To Be Published
PubMed: search

(-) 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 SEROGROUP B (STRAIN MC58)
    Organism Taxid: 122586
    Strain: MC58

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 35)

Asymmetric/Biological Unit (6, 35)
No.NameCountTypeFull Name
15HR1Ligand/Ion[(1R)-1-AMINO-2-(BENZYLAMINO)ETHYL]PHOSPHONIC ACID
2GOL4Ligand/IonGLYCEROL
3IMD1Ligand/IonIMIDAZOLE
4MSE18Mod. Amino AcidSELENOMETHIONINE
5SO410Ligand/IonSULFATE ION
6ZN1Ligand/IonZINC ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:293 , HIS A:297 , GLU A:316 , 5HR A:912binding site for residue ZN A 901
02AC2SOFTWAREARG A:781 , ARG A:822 , HOH A:1048 , HOH A:1149binding site for residue SO4 A 902
03AC3SOFTWAREARG A:636 , HOH A:1329 , HOH A:1464 , HOH A:1465 , HOH A:1492binding site for residue SO4 A 903
04AC4SOFTWARETHR A:565 , ARG A:568 , ARG A:569 , HOH A:1486binding site for residue SO4 A 904
05AC5SOFTWAREMSE A:469 , THR A:470 , ASP A:471 , HOH A:1101 , HOH A:1200 , HOH A:1342binding site for residue SO4 A 905
06AC6SOFTWAREALA A:331 , SER A:332 , HOH A:1373binding site for residue SO4 A 906
07AC7SOFTWARELEU A:402 , ARG A:406binding site for residue SO4 A 907
08AC8SOFTWAREALA A:191 , VAL A:192 , ASN A:831 , LYS A:838 , LYS A:842 , HOH A:1004 , HOH A:1021 , HOH A:1316binding site for residue SO4 A 908
09AC9SOFTWAREARG A:203binding site for residue SO4 A 909
10AD1SOFTWAREARG A:277 , HOH A:1366binding site for residue SO4 A 910
11AD2SOFTWAREGLN A:851 , GLU A:852 , GLY A:853binding site for residue SO4 A 911
12AD3SOFTWAREMSE A:103 , GLN A:115 , GLU A:117 , MSE A:256 , ALA A:258 , GLU A:260 , HIS A:293 , GLU A:294 , HIS A:297 , LYS A:315 , GLU A:316 , ASN A:369 , TYR A:377 , GLN A:818 , ZN A:901 , HOH A:1055binding site for residue 5HR A 912
13AD4SOFTWARETHR A:199 , ARG A:203 , TYR A:241 , ASP A:242 , LEU A:243 , ASP A:244 , HOH A:1328binding site for residue GOL A 913
14AD5SOFTWAREALA A:522binding site for residue GOL A 914
15AD6SOFTWARETHR A:282 , TRP A:712 , HOH A:1105 , HOH A:1377 , HOH A:1420binding site for residue GOL A 915
16AD7SOFTWAREASP A:242 , ARG A:303 , HOH A:1322 , HOH A:1466binding site for residue GOL A 916
17AD8SOFTWAREHIS A:24 , ARG A:37binding site for residue IMD A 917

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DYF)

(-) 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 5DYF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DYF)

(-) Exons   (0, 0)

(no "Exon" information available for 5DYF)

(-) 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:865
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               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..hhhhhhhhhh....eeeeeeeee..eeeeeeeee..............eeeeeeee.....ee.eee..eee..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
                 5dyf A   3 KTVHYLKDYQTPAYHILKTDLHFDINEPQTVVKSRLTVEPQRVGEPLVLDGSAKLLSVKINGAAADYVLEGETLTIAGVPSERFTVEVETEILPAENKSLmGLYASGGNLFTQCEPEGFRKITFYIDRPDVmSKFTTTIVADKKRYPVLLSNGNKIDGGEFSDGRHWVKWEDPFSKPSYLFALVAGDLAVTEDYFTTmSGRNVKIEFYTTEADKPKVGFAVESLKNAmKWDETRFGLEYDLDIFmVVAVGDFNmGAmENKGLNIFNTKFVLADSRTATDTDFEGIESVVGHEYFHNWTGNRVTCRDWFQLSLKEGLTVFRDQEFSGDRASRAVRRIENIRLLRQHQFPEDAGPTAHPVRPASYEEmNNFYTmTVYEKGAEVVRmYHTLLGEEGFQKGmKLYFQRHDGQAVTCDDFRAAmADANGINLDQFALWYSQAGTPVLEAEGRLKNNIFELTVKQTVPPTPDmTDKQPmmIPVKVGLLNRNGEAVAFDYQGKRATEAVLLLTEAEQTFLLEGVTEAVVPSLLRGFSAPVHLNYPYSDDDLLLLLAHDSDAFTRWEAAQTLYRRAVAANLATLSDGVELPKHEKLLAAVEKVISDDLLDNAFKALLLGVPSEAELWDGAENIDPLRYHQAREALLDTLAVHFLPKWHELNRQAAKQENQSYEYSPEAAGWRTLRNVCRAFVLRADPAHIETVAEKYGEmAQNmTHEWGILSAVNGNESDTRNRLLAQFADKFSDDALVmDKYFALVGSSRRSDTLQQVRTALQHPKFSLENPNKARSLIGSFSRNVPHFHAEDGSGYRFIADKVIEIDRFNPQVAARLVQAFNLCNKLEPHRKNLVKQALQRIRAQEGLSKDVGEIVGKILD 867
                                    12        22        32        42        52        62        72        82        92       102|      112       122       132 |     142       152       162       172       182       192       202       212       222       232       242    |  252   |  |262       272       282       292       302       312       322       332       342       352       362     | 372 |     382   |   392       402       412       422       432       442       452       462      |472  ||   482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702 |   | 712       722       732       742 |     752       762       772       782       792       802       812       822       832       842       852       862     
                                                                                                                              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 5DYF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DYF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DYF)

(-) 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 4qpe 4quo

(-) Related Entries Specified in the PDB File

4qir ANOTHER COMPLEX WITH A INHIBITOR RELATED ID: APC105593 RELATED DB: TARGETTRACK