Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF CYTOSOL AMINOPEPTIDASE FROM FRANCISELLA TULARENSIS
 
Authors :  N. Maltseva, Y. Kim, M. Gu, W. F. Anderson, A. Joachimiak, Center For S Genomics Of Infectious Diseases (Csgid)
Date :  26 Oct 10  (Deposition) - 01 Dec 10  (Release) - 01 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Alpha-Beta Sandwich, Aminopeptidase, Cytosol, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Maltseva, Y. Kim, M. Gu, W. F. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of Cytosol Aminopeptidase From Francisell Tularensis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CYTOSOL AMINOPEPTIDASE
    ChainsA
    EC Number3.4.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMCSG28
    Expression System StrainBL21 MAGIC
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    GeneFTT_1318C, PEPA
    Organism ScientificFRANCISELLA TULARENSIS SUBSP. TULARENSIS
    Organism Taxid177416
    StrainSCHU S4

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (6x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 44)

Asymmetric Unit (7, 44)
No.NameCountTypeFull Name
1CL5Ligand/IonCHLORIDE ION
2EDO10Ligand/Ion1,2-ETHANEDIOL
3FMT3Ligand/IonFORMIC ACID
4K3Ligand/IonPOTASSIUM ION
5MSE20Mod. Amino AcidSELENOMETHIONINE
6PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
7SO41Ligand/IonSULFATE ION
Biological Unit 1 (5, 216)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO60Ligand/Ion1,2-ETHANEDIOL
3FMT18Ligand/IonFORMIC ACID
4K-1Ligand/IonPOTASSIUM ION
5MSE120Mod. Amino AcidSELENOMETHIONINE
6PEG12Ligand/IonDI(HYDROXYETHYL)ETHER
7SO46Ligand/IonSULFATE ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:193 , TYR A:196 , PHE A:199 , HOH A:489BINDING SITE FOR RESIDUE K A 490
02AC2SOFTWAREASP A:154 , LYS A:157 , LEU A:290 , HOH A:730 , HOH A:731BINDING SITE FOR RESIDUE EDO A 491
03AC3SOFTWAREASN A:22 , LYS A:25 , ASP A:101 , GLU A:105BINDING SITE FOR RESIDUE PEG A 492
04AC4SOFTWARELYS A:79 , ASP A:370 , PRO A:405 , TYR A:406 , LYS A:409 , HOH A:526 , HOH A:710 , HOH A:739BINDING SITE FOR RESIDUE EDO A 493
05AC5SOFTWAREHOH A:698BINDING SITE FOR RESIDUE CL A 494
06AC6SOFTWAREARG A:336 , LEU A:360BINDING SITE FOR RESIDUE CL A 496
07AC7SOFTWAREGLN A:206 , GLY A:221 , SER A:224 , MSE A:226BINDING SITE FOR RESIDUE K A 497
08AC8SOFTWAREHOH A:836BINDING SITE FOR RESIDUE CL A 498
09AC9SOFTWAREGLU A:21 , ASN A:22 , PHE A:104 , GLU A:105BINDING SITE FOR RESIDUE FMT A 500
10BC1SOFTWAREARG A:118 , SER A:393 , ASN A:394 , ASP A:395 , ARG A:465 , PRO A:468 , HOH A:748 , HOH A:781BINDING SITE FOR RESIDUE FMT A 501
11BC2SOFTWARELYS A:352 , LEU A:382 , SER A:385 , GLU A:443 , TYR A:473 , GLN A:477BINDING SITE FOR RESIDUE EDO A 502
12BC3SOFTWAREGLN A:173 , ASN A:174 , ASP A:273 , MSE A:454BINDING SITE FOR RESIDUE EDO A 503
13BC4SOFTWAREASP A:370 , GLY A:451 , SER A:452 , GLY A:455 , SER A:463 , ARG A:465 , HOH A:552 , HOH A:671BINDING SITE FOR RESIDUE EDO A 504
14BC5SOFTWAREASN A:167 , HOH A:770BINDING SITE FOR RESIDUE CL A 505
15BC6SOFTWAREILE A:73 , GLU A:76 , LYS A:408 , HOH A:793 , HOH A:794BINDING SITE FOR RESIDUE EDO A 506
16BC7SOFTWAREMSE A:1 , ILE A:121 , THR A:124 , SER A:138 , LEU A:139 , HOH A:582 , HOH A:681BINDING SITE FOR RESIDUE EDO A 507
17BC8SOFTWAREALA A:210 , GLY A:213 , MSE A:214 , GLY A:215 , ARG A:222 , HOH A:714 , HOH A:715BINDING SITE FOR RESIDUE PEG A 508
18BC9SOFTWARELEU A:407 , GLU A:411BINDING SITE FOR RESIDUE FMT A 509
19CC1SOFTWAREALA A:389 , ALA A:392 , HIS A:472 , SER A:476 , HOH A:571 , HOH A:647 , HOH A:752BINDING SITE FOR RESIDUE EDO A 510
20CC2SOFTWAREILE A:179 , VAL A:317 , HOH A:754 , HOH A:866BINDING SITE FOR RESIDUE EDO A 511
21CC3SOFTWAREGLN A:87 , LYS A:90 , HOH A:867 , HOH A:868BINDING SITE FOR RESIDUE EDO A 512
22CC4SOFTWARELYS A:236 , PRO A:244 , HOH A:579 , HOH A:733 , HOH A:758BINDING SITE FOR RESIDUE SO4 A 513

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PEI)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Arg A:465 -Pro A:466

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PEI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PEI)

(-) Exons   (0, 0)

(no "Exon" information available for 3PEI)

(-) Sequences/Alignments

Asymmetric 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:456
 aligned with Q5NFC1_FRATT | Q5NFC1 from UniProtKB/TrEMBL  Length:479

    Alignment length:483
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           479   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479   
         Q5NFC1_FRATT     - -MKIVVNNQSTLAAELMIVAQENLQKLVEQTKCPNSKALLDRRIFKAKSGEVLPLLHGDKIVILLGLGLRQDFIASEYDKIIAKAAEQLKKLAIKEISVDIDYAFENDNVKQFTLDTVRALISETYVFDQLKTEKENYSLEQIELVYSGDQDIEDSAKIGSAIACGQNYAKDLQNLPANICTTDYMLNEARELTSKYATFSLDYLDQDAMAELGMGCALAVGRGSYMSNYTVCMEYKGGNEGDAPIVLVGKGLVFDNGGICIKQAAGMDSMKMDMGGVAAVMGTMKAIAMLNLPVNVVGVMGLAENAVDARSYRPGDVLKSMKGITVEVSNTDAEGRLVLCDTLTYIGKYKPKAVIDLATLTGAMIISLGDAYSGMFANSDKLANSLEQAANASNDLIWRLPLHKPYLKKIESKVADMDNCGRDRSAGSIVAALFLSKFTEDYEWAHLDIAGSAMGDFASCKASGRPVPLLVHYLISQAK---   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------Peptidase_M17_N-3peiA        01 A:10-134                                                                                     -------------------------------Peptidase_M17-3peiA02 A:166-472                                                                                                                                                                                                                                                                                    ---------- Pfam domains
         Sec.struct. author ..eeeee......eeeeeehhhhhhhhhhhh--------............eeee.....eeeeee..hhhhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhhhhh................eeeee......hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhhh......eeeeeeee........eeeeeeeee....------------....hhhhhhhhhhhhhhhhhh...eeeeeeeeee.------....eeee.....eeee.hhhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhh...eeeee.hhhhhhhhhhhhhhhh..eee...hhhhhhhhh.....ee.......hhhhhhhhhhhh......eeeeehhhhhhh.-........hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pei A   0 mmKIVVNNQSTLAAELmIVAQENLQKLVEQT--------LDRRIFKAKSGEVLPLLHGDKIVILLGLGLRQDFIASEYDKIIAKAAEQLKKLAIKEISVDIDYAFENDNVKQFTLDTVRALISETYVFDQLKTEKENYSLEQIELVYSGDQDIEDSAKIGSAIACGQNYAKDLQNLPANICTTDYmLNEARELTSKYATFSLDYLDQDAmAELGmGCALAVGRGSYmSNYTVCmEYKGGNEGDAPIVLVGKGLVFDNG------------mKmDmGGVAAVmGTmKAIAmLNLPVNVVGVmGLAEN------YRPGDVLKSmKGITVEVSNTDAEGRLVLCDTLTYIGKYKPKAVIDLATLTGAmIISLGDAYSGmFANSDKLANSLEQAANASNDLIWRLPLHKPYLKKIESKVADmDNCGRDRSAGSIVAALFLSKFTEDYEWAHLDIAGSAmGD-ASCKASGRPVPLLVHYLISQAKENL 482
                            ||       9      | 19        29|       39        49        59        69        79        89        99       109       119       129       139       149       159       169       179     | 189       199       209    |  219      |229   |   239       249       | -         -| | |  279 |  |  289       299|    |   -  |    319 |     329       339       349       359    |  369     | 379       389       399       409       419       429       439       449    | |459       469       479   
                            ||             16-MSE        30       39                                                                                                                                               185-MSE                 209-MSE|         226-MSE  |                     257          270-MSE      |  |    |        300-MSE5    312      321-MSE                                    364-MSE    375-MSE                                   417-MSE                              454-MSE                        
                            0-MSE                                                                                                                                                                                                               214-MSE            233-MSE                                272-MSE    |  |    |                                                                                                                                                                    456 |                        
                             1-MSE                                                                                                                                                                                                                                                                          274-MSE  |  |    |                                                                                                                                                                      458                        
                                                                                                                                                                                                                                                                                                                   281-MSE   |                                                                                                                                                                                                 
                                                                                                                                                                                                                                                                                                                      284-MSE|                                                                                                                                                                                                 
                                                                                                                                                                                                                                                                                                                           289-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 3PEI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PEI)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: MACRO (14)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q5NFC1_FRATT | Q5NFC1)
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:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008235    metalloexopeptidase activity    Catalysis of the hydrolysis of a peptide bond not more than three residues from the N- or C-terminus of a polypeptide chain 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:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
    GO:0019538    protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

 Visualization

(-) Interactive Views

Asymmetric 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FMT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    K  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
    CC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:465 - Pro A:466   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3pei
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q5NFC1_FRATT | Q5NFC1
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.4.11.1
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  Q5NFC1_FRATT | Q5NFC1
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3PEI)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3PEI)