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 FROM HUMAN PATHOGEN NEISSERIA MENINGITIDIS
 
Authors :  B. Nocek, R. Mulligan, M. Bargassa, A. Joachimiak, Midwest Center Fo Structural Genomics (Mcsg)
Date :  28 Apr 06  (Deposition) - 30 May 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A
Keywords :  Alanine Aminopeptidase, Aminopeptidase N, M1 Family Peptidases, Mcsg, Psi-2, Structural Genomics, Protein Structure Initiative, Midwest Center For Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Nocek, R. Mulligan, M. Bargassa, F. Collart, A. Joachimiak
Crystal Structure Of Aminopeptidase N From Human Pathogen Neisseria Meningitidis.
Proteins V. 70 273 2007
PubMed-ID: 17876832  |  Reference-DOI: 10.1002/PROT.21276

(-) Compounds

Molecule 1 - AMINOPEPTIDASE N
    Chains: A
    EC Number: 3.4.11.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PET15B
    Organism Scientific: NEISSERIA MENINGITIDIS
    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  (3, 35)

Asymmetric/Biological Unit (3, 35)
No.NameCountTypeFull Name
1MSE18Mod. Amino AcidSELENOMETHIONINE
2SO416Ligand/IonSULFATE ION
3ZN1Ligand/IonZINC ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:293 , HIS A:297 , GLU A:316 , HOH A:1411BINDING SITE FOR RESIDUE ZN A 1001
02AC2SOFTWAREARG A:636 , HOH A:1031 , HOH A:1056 , HOH A:1678 , HOH A:1694BINDING SITE FOR RESIDUE SO4 A 901
03AC3SOFTWAREMSE A:469 , THR A:470 , ASP A:471 , HOH A:1002 , HOH A:1279 , HOH A:1412 , HOH A:1632 , HOH A:1698BINDING SITE FOR RESIDUE SO4 A 902
04AC4SOFTWAREALA A:191 , VAL A:192 , ASN A:831 , LYS A:838 , LYS A:842 , HOH A:1020 , HOH A:1344 , HOH A:1629BINDING SITE FOR RESIDUE SO4 A 903
05AC5SOFTWAREARG A:330 , HOH A:1726BINDING SITE FOR RESIDUE SO4 A 904
06AC6SOFTWARELEU A:402 , ARG A:406BINDING SITE FOR RESIDUE SO4 A 905
07AC7SOFTWAREALA A:492 , ARG A:499BINDING SITE FOR RESIDUE SO4 A 906
08AC8SOFTWAREGLY A:497 , ARG A:499BINDING SITE FOR RESIDUE SO4 A 907
09AC9SOFTWAREGLU A:521 , ALA A:522BINDING SITE FOR RESIDUE SO4 A 908
10BC1SOFTWARETHR A:565 , ARG A:568 , ARG A:569 , HOH A:1710BINDING SITE FOR RESIDUE SO4 A 909
11BC2SOFTWARETHR A:212 , ASP A:215 , HOH A:1105 , HOH A:1456 , HOH A:1651BINDING SITE FOR RESIDUE SO4 A 910
12BC3SOFTWAREARG A:449 , LEU A:450BINDING SITE FOR RESIDUE SO4 A 911
13BC4SOFTWAREALA A:331 , SER A:332 , HOH A:1246BINDING SITE FOR RESIDUE SO4 A 912
14BC5SOFTWAREARG A:361 , HOH A:1420 , HOH A:1474 , HOH A:1539BINDING SITE FOR RESIDUE SO4 A 913
15BC6SOFTWARESER A:773 , LEU A:774 , HOH A:1202BINDING SITE FOR RESIDUE SO4 A 914
16BC7SOFTWAREMSE A:256 , GLY A:257 , LYS A:270 , ARG A:781BINDING SITE FOR RESIDUE SO4 A 915
17BC8SOFTWARETYR A:372BINDING SITE FOR RESIDUE SO4 A 916

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GTQ)

(-) 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 2GTQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2GTQ)

(-) Exons   (0, 0)

(no "Exon" information available for 2GTQ)

(-) 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:864
 aligned with Q9JYV4_NEIMB | Q9JYV4 from UniProtKB/TrEMBL  Length:867

    Alignment length:864
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863    
         Q9JYV4_NEIMB     4 TVHYLKDYQTPAYHILKTDLHFDINEPQTVVKSRLTVEPQRVGEPLVLDGSAKLLSVKINGAAADYVLEGETLTIAGVPSERFTVEVETEILPAENKSLMGLYASGGNLFTQCEPEGFRKITFYIDRPDVMSKFTTTIVADKKRYPVLLSNGNKIDGGEFSDGRHWVKWEDPFSKPSYLFALVAGDLAVTEDYFTTMSGRNVKIEFYTTEADKPKVGFAVESLKNAMKWDETRFGLEYDLDIFMVVAVGDFNMGAMENKGLNIFNTKFVLADSRTATDTDFEGIESVVGHEYFHNWTGNRVTCRDWFQLSLKEGLTVFRDQEFSGDRASRAVRRIENIRLLRQHQFPEDAGPTAHPVRPASYEEMNNFYTMTVYEKGAEVVRMYHTLLGEEGFQKGMKLYFQRHDGQAVTCDDFRAAMADANGINLDQFALWYSQAGTPVLEAEGRLKNNIFELTVKQTVPPTPDMTDKQPMMIPVKVGLLNRNGEAVAFDYQGKRATEAVLLLTEAEQTFLLEGVTEAVVPSLLRGFSAPVHLNYPYSDDDLLLLLAHDSDAFTRWEAAQTLYRRAVAANLATLSDGVELPKHEKLLAAVEKVISDDLLDNAFKALLLGVPSEAELWDGAENIDPLRYHQAREALLDTLAVHFLPKWHELNRQAAKQENQSYEYSPEAAGWRTLRNVCRAFVLRADPAHIETVAEKYGEMAQNMTHEWGILSAVNGNESDTRNRLLAQFADKFSDDALVMDKYFALVGSSRRSDTLQQVRTALQHPKFSLENPNKARSLIGSFSRNVPHFHAEDGSGYRFIADKVIEIDRFNPQVAARLVQAFNLCNKLEPHRKNLVKQALQRIRAQEGLSKDVGEIVGKILD 867
               SCOP domains d2gtqa1 A:4-188 Aminopeptidase N (APN) N-terminal domain                                                                                                                                 d2gtqa2 A:189-438 Aminopeptidase N (APN) catalytic domain                                                                                                                                                                                                 d2gtqa3 A:439-539 Aminopeptidase N (APN) domain 3                                                    d2gtqa4 A:540-866 Aminopeptidase N (APN) C-terminal domain                                                                                                                                                                                                                                                                             - SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2gtqA05 A:541-867 Metalloproteases ('zincins'), catalytic domain                                                                                                                                                                                                                                                                        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..eehhhhhhhhhhhhh...hhhhhhhhhh....eeeeeeeee..eeeeeeeee..............eeeeeeee........ee....ee..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
                 2gtq A   4 TVHYLKDYQTPAYHILKTDLHFDINEPQTVVKSRLTVEPQRVGEPLVLDGSAKLLSVKINGAAADYVLEGETLTIAGVPSERFTVEVETEILPAENKSLmGLYASGGNLFTQCEPEGFRKITFYIDRPDVmSKFTTTIVADKKRYPVLLSNGNKIDGGEFSDGRHWVKWEDPFSKPSYLFALVAGDLAVTEDYFTTmSGRNVKIEFYTTEADKPKVGFAVESLKNAmKWDETRFGLEYDLDIFmVVAVGDFNmGAmENKGLNIFNTKFVLADSRTATDTDFEGIESVVGHEYFHNWTGNRVTCRDWFQLSLKEGLTVFRDQEFSGDRASRAVRRIENIRLLRQHQFPEDAGPTAHPVRPASYEEmNNFYTmTVYEKGAEVVRmYHTLLGEEGFQKGmKLYFQRHDGQAVTCDDFRAAmADANGINLDQFALWYSQAGTPVLEAEGRLKNNIFELTVKQTVPPTPDmTDKQPmmIPVKVGLLNRNGEAVAFDYQGKRATEAVLLLTEAEQTFLLEGVTEAVVPSLLRGFSAPVHLNYPYSDDDLLLLLAHDSDAFTRWEAAQTLYRRAVAANLATLSDGVELPKHEKLLAAVEKVISDDLLDNAFKALLLGVPSEAELWDGAENIDPLRYHQAREALLDTLAVHFLPKWHELNRQAAKQENQSYEYSPEAAGWRTLRNVCRAFVLRADPAHIETVAEKYGEmAQNmTHEWGILSAVNGNESDTRNRLLAQFADKFSDDALVmDKYFALVGSSRRSDTLQQVRTALQHPKFSLENPNKARSLIGSFSRNVPHFHAEDGSGYRFIADKVIEIDRFNPQVAARLVQAFNLCNKLEPHRKNLVKQALQRIRAQEGLSKDVGEIVGKILD 867
                                    13        23        33        43        53        63        73        83        93       103       113       123       133|      143       153       163       173       183       193      |203       213       223      |233       243   |   253  |  | 263       273       283       293       303       313       323       333       343       353       363    |  373|      383  |    393      |403       413       423       433       443       453       463     | 473 ||    483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703|   |  713       723       733       743|      753       763       773       783       793       803       813       823       833       843       853       863    
                                                                                                                             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  (4, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GTQ)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9JYV4_NEIMB | Q9JYV4)
molecular function
    GO:0004177    aminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

 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
    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 ]
 
  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
  2gtq
    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
  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
  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: 4pu2 4pvb 4pw4 4qhp 4qir 4qme 4qpe 4quo 5dyf

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2GTQ)