Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF AMINOPEPTIDASE N IN COMPLEX WITH THE PHOSPHINIC DIPEPTIDE ANALOGUE LL-(R,S)-HPHEP[CH2]PHE(3-CH2NH2)
 
Authors :  B. Nocek, R. Mulligan, A. Joachimak, S. Vassiliou, L. Berlicki, A. Much
Date :  11 Jul 14  (Deposition) - 10 Sep 14  (Release) - 22 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  M1 Family Aminopeptidase, Metalloprotease, Apn, 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 BL21(DE3)
    Expression System Taxid: 469008
    Gene: PEPN, NMBH4476_0804, NMH_0477
    Organism Scientific: NEISSERIA MENINGITIDIS MC58
    Organism Taxid: 122586
    Synonym: MEMBRANE ALANYL AMINOPEPTIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 36)

Asymmetric/Biological Unit (6, 36)
No.NameCountTypeFull Name
13DZ2Ligand/Ion(2S)-2-[3-(AMINOMETHYL)BENZYL]-3-[(R)-[(1R)-1-AMINO-3-PHENYLPROPYL](HYDROXY)PHOSPHORYL]PROPANOIC ACID
2GOL4Ligand/IonGLYCEROL
3IMD1Ligand/IonIMIDAZOLE
4MSE18Mod. Amino AcidSELENOMETHIONINE
5SO410Ligand/IonSULFATE ION
6ZN1Ligand/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 , ZN A:907 , HOH A:1210 , HOH A:1562BINDING SITE FOR RESIDUE 3DZ A 901
02AC2SOFTWAREASP A:604 , ASN A:605 , ALA A:606 , GLU A:671 , TRP A:675 , HOH A:1948BINDING SITE FOR RESIDUE GOL A 902
03AC3SOFTWARESER A:542 , ASP A:543 , ASP A:544 , LYS A:589 , HOH A:1763BINDING SITE FOR RESIDUE GOL A 903
04AC4SOFTWARETHR A:282 , TRP A:712 , HOH A:1090 , HOH A:1299 , HOH A:1668 , HOH A:1685 , HOH A:1793 , HOH A:1859 , HOH A:1914BINDING SITE FOR RESIDUE GOL A 904
05AC5SOFTWAREPHE A:163 , SER A:164BINDING SITE FOR RESIDUE GOL A 905
06AC6SOFTWAREASP A:22 , ARG A:37BINDING SITE FOR RESIDUE IMD A 906
07AC7SOFTWAREHIS A:293 , HIS A:297 , GLU A:316 , 3DZ A:901BINDING SITE FOR RESIDUE ZN A 907
08AC8SOFTWAREASN A:156 , PRO A:175 , PHE A:176 , ARG A:203 , ASN A:204 , TYR A:241 , ASP A:242 , LEU A:243 , ASP A:244 , HOH A:1026 , HOH A:1140 , HOH A:1488 , HOH A:1553 , HOH A:1882 , HOH A:1894 , HOH A:1931 , HOH A:2025BINDING SITE FOR RESIDUE 3DZ A 908
09AC9SOFTWAREMSE A:469 , THR A:470 , ASP A:471 , HOH A:1083 , HOH A:1225 , HOH A:1618 , HOH A:1656 , HOH A:1682BINDING SITE FOR RESIDUE SO4 A 909
10BC1SOFTWARETHR A:565 , ARG A:568 , ARG A:569 , HOH A:1584 , HOH A:1727 , HOH A:1854 , HOH A:1866BINDING SITE FOR RESIDUE SO4 A 910
11BC2SOFTWAREARG A:449 , LEU A:450 , HOH A:1659 , HOH A:1709BINDING SITE FOR RESIDUE SO4 A 911
12BC3SOFTWAREALA A:191 , VAL A:192 , ASN A:831 , LYS A:838 , LYS A:842 , HOH A:1196 , HOH A:1441 , HOH A:1490BINDING SITE FOR RESIDUE SO4 A 912
13BC4SOFTWAREARG A:499 , HOH A:1977BINDING SITE FOR RESIDUE SO4 A 913
14BC5SOFTWAREARG A:636 , ARG A:755 , HOH A:1117 , HOH A:1847 , HOH A:1869 , HOH A:1875BINDING SITE FOR RESIDUE SO4 A 914
15BC6SOFTWARELYS A:3 , GLY A:161 , GLU A:162 , HOH A:1198BINDING SITE FOR RESIDUE SO4 A 915
16BC7SOFTWAREALA A:331 , SER A:332 , HOH A:1407 , HOH A:1767BINDING SITE FOR RESIDUE SO4 A 916
17BC8SOFTWARELEU A:402 , ARG A:406BINDING SITE FOR RESIDUE SO4 A 917
18BC9SOFTWAREGLU A:521 , ALA A:522 , HOH A:1940BINDING SITE FOR RESIDUE SO4 A 918

(-) SS Bonds  (0, 0)

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

(-) 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 4QUO)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QUO)

(-) 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..........eeeeeeeeee.....eeee..eeeeeee....eeeeeeeeeeeehhhhh.eeee..eeeeeeee.....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee......ee....eeeee.hhh.......hhhhhhhhhhhhhhhhhh.......ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhh...hhhhhhhhhh....eeeeeeeee..eeeeeeeee..............eeeeeeee........eee..eee..eeeee...eeeeee.......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
                 4quo 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 4QUO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 11)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    3DZ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IMD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:117 - Pro A:118   [ RasMol ]  
    Glu A:29 - Pro A:30   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4quo
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  E6MUM9_NEIMH | E6MUM9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  Q9JYV4_NEIMB | Q9JYV4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.4.11.2
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  E6MUM9_NEIMH | E6MUM9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q9JYV4_NEIMB | Q9JYV4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q9JYV4_NEIMB | Q9JYV4: 2gtq 4pu2 4pvb 4pw4 4qhp 4qir 4qme 4qpe 5dyf

(-) Related Entries Specified in the PDB File

2gtq 4qhp 4qme