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 THE N-TERMINAL BETA-AMINOPEPTIDASE BAPA IN COMPLEX WITH AMPICILLIN
 
Authors :  T. Merz, T. Heck, B. Geueke, H. -P. E. Kohler, M. G. Gruetter
Date :  08 Jun 10  (Deposition) - 28 Sep 11  (Release) - 28 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ntn-Hydrolase, Beta-Aminopeptidase, Beta-Peptide, Alpha-Beta-Beta- Alpha Sandwich, N-Terminal Beta-Aminopeptidase, Hydrolase-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Heck, T. Merz, B. Geueke, M. G. Gruetter, H. -P. E. Kohler
Crystal Structures And Inhibition Of The Beta-Aminopeptidas Bapa, A New Ampicillin-Recognizing Member Of The N-Terminal Nucleophile Hydrolase Family
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BETA-PEPTIDYL AMINOPEPTIDASE
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPYBAPA
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid469008
    Expression System Vector TypePET3C
    GeneBAPA
    Organism ScientificSPHINGOSINICELLA XENOPEPTIDILYTICA
    Organism Taxid364098
    Strain3-2W4

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1AIC4Ligand/Ion(2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID
2GOL4Ligand/IonGLYCEROL
3NDV2Ligand/Ion(2S,4S)-2-[(1R)-1-{[(2R)-2-AMINO-2-PHENYLACETYL]AMINO}-2-OXOETHYL]-5,5-DIMETHYL-1,3-THIAZOLIDINE-4-CARBOXYLICACID

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:88 , GLY A:89 , GLN A:90 , PRO A:263 , HIS A:299 , ILE A:301 , PRO A:307 , MET C:262 , HIS C:264 , ASP C:315BINDING SITE FOR RESIDUE GOL A 374
02AC2SOFTWARETHR A:76 , GLU A:133 , THR A:134 , LEU A:135 , ARG A:138 , SER A:250 , LEU A:287 , SER A:288 , NDV A:376 , HOH A:390 , HOH A:628 , PHE B:124BINDING SITE FOR RESIDUE AIC A 375
03AC3SOFTWAREARG A:138 , VAL A:232 , ALA A:237 , ALA A:238 , AIC A:375BINDING SITE FOR RESIDUE NDV A 376
04AC4SOFTWAREVAL B:88 , GLY B:89 , GLN B:90 , PRO B:263 , HIS B:299 , ILE B:301 , PRO B:307 , MET D:262 , HIS D:264 , ASP D:315BINDING SITE FOR RESIDUE GOL B 374
05AC5SOFTWAREMET B:262 , HIS B:264 , ASP B:315 , VAL D:88 , GLY D:89 , GLN D:90 , PRO D:263 , HIS D:299 , ILE D:301 , PRO D:307BINDING SITE FOR RESIDUE GOL B 375
06AC6SOFTWAREPHE A:124 , THR B:76 , GLY B:77 , GLU B:133 , LEU B:135 , ASN B:137 , ARG B:138 , SER B:250 , LEU B:287 , SER B:288 , HOH B:400 , HOH B:930BINDING SITE FOR RESIDUE AIC B 376
07AC7SOFTWAREMET A:262 , HIS A:264 , ASP A:315 , VAL C:88 , GLY C:89 , GLN C:90 , PRO C:263 , HIS C:299 , ILE C:301 , PRO C:307BINDING SITE FOR RESIDUE GOL C 374
08AC8SOFTWARETHR C:76 , GLY C:77 , GLU C:133 , LEU C:135 , ASN C:137 , ARG C:138 , SER C:250 , LEU C:287 , HOH C:386 , HOH C:836 , HOH C:950 , PHE D:124BINDING SITE FOR RESIDUE AIC C 375
09AC9SOFTWAREPHE C:124 , THR D:76 , GLY D:77 , GLU D:133 , LEU D:135 , ARG D:138 , SER D:250 , LEU D:287 , SER D:288 , NDV D:375 , HOH D:396 , HOH D:708BINDING SITE FOR RESIDUE AIC D 374
10BC1SOFTWAREARG D:138 , VAL D:232 , ALA D:237 , ALA D:238 , AIC D:374BINDING SITE FOR RESIDUE NDV D 375

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:46 -Pro A:47
2Gly B:46 -Pro B:47
3Gly C:46 -Pro C:47
4Gly D:46 -Pro D:47

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NDV)

(-) 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:367
 aligned with BAPA_SPHXN | Q52VH2 from UniProtKB/Swiss-Prot  Length:402

    Alignment length:371
                                    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 
           BAPA_SPHXN    30 GPRARDLGVPFEGTPGALNAITDVAGVEVGHTTVISGDGAMVIGKGPYRTGVTIIHPLGKTSLDGVAAGRAVINGTGEWTGMHLVDEVGQFLGPIALTGTGNVGLVHQSMMDWSVGKVPEEALFSRLLPVVAETLDNRLNDVFGHGLTRDHVFAALDGAKGGPVAEGNVGGGTGMIAYTFKGGIGTSSRVVSAGDTRYTVGVLVQANHGDRNDLRIAGVQIGKEIKGAWPEVNGIVAAGPDAGKPQDKNSLLIVIATDAPLMPHQLERMARRAALGVGRNGSTAGALSGEFALAFSTSHVIPLGGKPRLPAIINDTDSETMNALFRGVVQATEEALVNQLVASETMTGANNAKVYGIPHDQLARIMKARFP 400
               SCOP domains d3ndva_ A: automated matches                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh...........hhhhh...eeeeeeeee...........eeeeeeeee........eeeeeeeeee......hhhhhhhhheee..eeeee..hhhhhhhhhhhhhh......hhhhhh..eeeee.............hhhhhhhhhhhh.........hhhhh..ee..ee.eeeeeeeeeee..eeeeeeeeeee........ee..ee..........ee..ee.........----.eeeeeee....hhhhhhhhhhhhhhhhhhh.........eeeeeeeeeeee...............hhhhhhhhhhhhhhhhhhhhhhhhhhh..ee....eee...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ndv A   1 GPRARDLGVPFEGTPGALNAITDVAGVEVGHTTVISGDGAMVIGKGPYRTGVTIIHPLGKTSLDGVAAGRAVINGTGEWTGMHLVDEVGQFLGPIALTGTGNVGLVHQSMMDWSVGKVPEEALFSRLLPVVAETLDNRLNDVFGHGLTRDHVFAALDGAKGGPVAEGNVGGGTGMIAYTFKGGIGTSSRVVSAGDTRYTVGVLVQANHGDRNDLRIAGVQIGKEIKGAWPEVNGIVAAGPDAGKP----SLLIVIATDAPLMPHQLERMARRAALGVGRNGSTAGALSGEFALAFSTSHVIPLGGKPRLPAIINDTDSETMNALFRGVVQATEEALVNQLVASETMTGANNAKVYGIPHDQLARIMKARFP 371
                                    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 
                                                                                                                                                                                                                                                                              245  250                                                                                                                         

Chain B from PDB  Type:PROTEIN  Length:365
 aligned with BAPA_SPHXN | Q52VH2 from UniProtKB/Swiss-Prot  Length:402

    Alignment length:371
                                    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 
           BAPA_SPHXN    30 GPRARDLGVPFEGTPGALNAITDVAGVEVGHTTVISGDGAMVIGKGPYRTGVTIIHPLGKTSLDGVAAGRAVINGTGEWTGMHLVDEVGQFLGPIALTGTGNVGLVHQSMMDWSVGKVPEEALFSRLLPVVAETLDNRLNDVFGHGLTRDHVFAALDGAKGGPVAEGNVGGGTGMIAYTFKGGIGTSSRVVSAGDTRYTVGVLVQANHGDRNDLRIAGVQIGKEIKGAWPEVNGIVAAGPDAGKPQDKNSLLIVIATDAPLMPHQLERMARRAALGVGRNGSTAGALSGEFALAFSTSHVIPLGGKPRLPAIINDTDSETMNALFRGVVQATEEALVNQLVASETMTGANNAKVYGIPHDQLARIMKARFP 400
               SCOP domains d3ndvb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh...........hhhhh...eeeeeeeee...........eeeeeeeee........eeeeeeeeee......hhhhhhhhheee..eeeee..hhhhhhhhhhhhhh...hhhhhhhhh..eeeee.............hhhhhhhhhhhh.........hhhhh..ee..ee.eeeeeeeeeee..eeeeeeeeeee........ee..ee..........ee..ee.......------.eeeeeee....hhhhhhhhhhhhhhhhhhh.........eeeeeeeeeeee...............hhhhhhhhhhhhhhhhhhhhhhhhhhh..ee....eee...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ndv B   1 GPRARDLGVPFEGTPGALNAITDVAGVEVGHTTVISGDGAMVIGKGPYRTGVTIIHPLGKTSLDGVAAGRAVINGTGEWTGMHLVDEVGQFLGPIALTGTGNVGLVHQSMMDWSVGKVPEEALFSRLLPVVAETLDNRLNDVFGHGLTRDHVFAALDGAKGGPVAEGNVGGGTGMIAYTFKGGIGTSSRVVSAGDTRYTVGVLVQANHGDRNDLRIAGVQIGKEIKGAWPEVNGIVAAGPDAG------SLLIVIATDAPLMPHQLERMARRAALGVGRNGSTAGALSGEFALAFSTSHVIPLGGKPRLPAIINDTDSETMNALFRGVVQATEEALVNQLVASETMTGANNAKVYGIPHDQLARIMKARFP 371
                                    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 
                                                                                                                                                                                                                                                                            243    250                                                                                                                         

Chain C from PDB  Type:PROTEIN  Length:366
 aligned with BAPA_SPHXN | Q52VH2 from UniProtKB/Swiss-Prot  Length:402

    Alignment length:371
                                    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 
           BAPA_SPHXN    30 GPRARDLGVPFEGTPGALNAITDVAGVEVGHTTVISGDGAMVIGKGPYRTGVTIIHPLGKTSLDGVAAGRAVINGTGEWTGMHLVDEVGQFLGPIALTGTGNVGLVHQSMMDWSVGKVPEEALFSRLLPVVAETLDNRLNDVFGHGLTRDHVFAALDGAKGGPVAEGNVGGGTGMIAYTFKGGIGTSSRVVSAGDTRYTVGVLVQANHGDRNDLRIAGVQIGKEIKGAWPEVNGIVAAGPDAGKPQDKNSLLIVIATDAPLMPHQLERMARRAALGVGRNGSTAGALSGEFALAFSTSHVIPLGGKPRLPAIINDTDSETMNALFRGVVQATEEALVNQLVASETMTGANNAKVYGIPHDQLARIMKARFP 400
               SCOP domains d3ndvc_ C: automated matches                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh...........hhhhh...eeeeeeeee...........eeeeeeeee........eeeeeeeeee......hhhhhhhhheee..eeeee..hhhhhhhhhhhhhh...hhhhhhhhh..eeeee.............hhhhhhhhhhhh.........hhhhh..ee..ee.eeeeeeeeeee..eeeeeeeeeee........ee..ee..........ee..ee........-----.eeeeeee....hhhhhhhhhhhhhhhhhhh.........eeeeeeeeeeee...............hhhhhhhhhhhhhhhhhhhhhhhhhhh..ee....eee...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ndv C   1 GPRARDLGVPFEGTPGALNAITDVAGVEVGHTTVISGDGAMVIGKGPYRTGVTIIHPLGKTSLDGVAAGRAVINGTGEWTGMHLVDEVGQFLGPIALTGTGNVGLVHQSMMDWSVGKVPEEALFSRLLPVVAETLDNRLNDVFGHGLTRDHVFAALDGAKGGPVAEGNVGGGTGMIAYTFKGGIGTSSRVVSAGDTRYTVGVLVQANHGDRNDLRIAGVQIGKEIKGAWPEVNGIVAAGPDAGK-----SLLIVIATDAPLMPHQLERMARRAALGVGRNGSTAGALSGEFALAFSTSHVIPLGGKPRLPAIINDTDSETMNALFRGVVQATEEALVNQLVASETMTGANNAKVYGIPHDQLARIMKARFP 371
                                    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 
                                                                                                                                                                                                                                                                             244   250                                                                                                                         

Chain D from PDB  Type:PROTEIN  Length:367
 aligned with BAPA_SPHXN | Q52VH2 from UniProtKB/Swiss-Prot  Length:402

    Alignment length:371
                                    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 
           BAPA_SPHXN    30 GPRARDLGVPFEGTPGALNAITDVAGVEVGHTTVISGDGAMVIGKGPYRTGVTIIHPLGKTSLDGVAAGRAVINGTGEWTGMHLVDEVGQFLGPIALTGTGNVGLVHQSMMDWSVGKVPEEALFSRLLPVVAETLDNRLNDVFGHGLTRDHVFAALDGAKGGPVAEGNVGGGTGMIAYTFKGGIGTSSRVVSAGDTRYTVGVLVQANHGDRNDLRIAGVQIGKEIKGAWPEVNGIVAAGPDAGKPQDKNSLLIVIATDAPLMPHQLERMARRAALGVGRNGSTAGALSGEFALAFSTSHVIPLGGKPRLPAIINDTDSETMNALFRGVVQATEEALVNQLVASETMTGANNAKVYGIPHDQLARIMKARFP 400
               SCOP domains d3ndvd_ D: automated matches                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh...........hhhhh...eeeeeeeee...........eeeeeeeee........eeeeeeeeee......hhhhhhhhheee..eeeee..hhhhhhhhhhhhhh...hhhhhhhhh..eeeee.............hhhhhhhhhhhh.........hhhhh..ee..ee.eeeeeeeeeee..eeeeeeeeeee........ee..ee..........ee..ee.........----.eeeeeee....hhhhhhhhhhhhhhhhhhh.........eeeeeeeeeeee...............hhhhhhhhhhhhhhhhhhhhhhhhhhh..ee....eee...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ndv D   1 GPRARDLGVPFEGTPGALNAITDVAGVEVGHTTVISGDGAMVIGKGPYRTGVTIIHPLGKTSLDGVAAGRAVINGTGEWTGMHLVDEVGQFLGPIALTGTGNVGLVHQSMMDWSVGKVPEEALFSRLLPVVAETLDNRLNDVFGHGLTRDHVFAALDGAKGGPVAEGNVGGGTGMIAYTFKGGIGTSSRVVSAGDTRYTVGVLVQANHGDRNDLRIAGVQIGKEIKGAWPEVNGIVAAGPDAGKP----SLLIVIATDAPLMPHQLERMARRAALGVGRNGSTAGALSGEFALAFSTSHVIPLGGKPRLPAIINDTDSETMNALFRGVVQATEEALVNQLVASETMTGANNAKVYGIPHDQLARIMKARFP 371
                                    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 
                                                                                                                                                                                                                                                                              245  250                                                                                                                         

   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  (1, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3NDV)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (BAPA_SPHXN | Q52VH2)
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: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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

 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
    AIC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NDV  [ 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 ]
 
  Cis Peptide Bonds
    Gly A:46 - Pro A:47   [ RasMol ]  
    Gly B:46 - Pro B:47   [ RasMol ]  
    Gly C:46 - Pro C:47   [ RasMol ]  
    Gly D:46 - Pro D:47   [ RasMol ]  
 

(-) 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
  3ndv
    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
  BAPA_SPHXN | Q52VH2
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  BAPA_SPHXN | Q52VH2
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        BAPA_SPHXN | Q52VH23n2w 3n33 3n5i 3nfb

(-) Related Entries Specified in the PDB File

1b65 D/L-AMINOPEPTIDASE DMPA FROM O. ANTHROPI
3n2w NATIVE ENZYME
3n33 BAPA IN COMPLEX WITH PEFABLOC SC