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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ACYLPEPTIDE HYDROLASE/ESTERASE FROM AEROPYRUM PERNIX K1 IN COMPLEX WITH P-NITROPHENYL PHOSPHATE
 
Authors :  M. Bartlam, G. Wang, R. Gao, H. Yang, X. Zhao, G. Xie, S. Cao, Y. Feng, Z. Ra
Date :  27 Mar 04  (Deposition) - 02 Nov 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta Propeller Domain, Alpha/Beta Hydrolase Domain, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Bartlam, G. Wang, H. Yang, R. Gao, X. Zhao, G. Xie, S. Cao, Y. Feng, Z. Rao
Crystal Structure Of An Acylpeptide Hydrolase/Esterase From Aeropyrum Pernix K1
Structure V. 12 1481 2004
PubMed-ID: 15296741  |  Reference-DOI: 10.1016/J.STR.2004.05.019

(-) Compounds

Molecule 1 - ACYLAMINO-ACID-RELEASING ENZYME
    ChainsA, B
    EC Number3.4.19.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificAEROPYRUM PERNIX
    Organism Taxid56636
    SynonymAARE, ACYL-PEPTIDE HYDROLASE, APH, ACYLAMINOACYL-PEPTIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
14NP2Ligand/Ion4-NITROPHENYL PHOSPHATE
2GOL1Ligand/IonGLYCEROL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
14NP1Ligand/Ion4-NITROPHENYL PHOSPHATE
2GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
14NP1Ligand/Ion4-NITROPHENYL PHOSPHATE
2GOL-1Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:369 , SER A:445 , TRP A:474 , MET A:477 , PHE A:485 , PHE A:488 , ILE A:489 , ARG A:526 , THR A:527 , HIS A:556BINDING SITE FOR RESIDUE 4NP A 701
2AC2SOFTWAREGLY B:369 , SER B:445 , TRP B:474 , MET B:477 , PHE B:485 , ILE B:489 , THR B:527 , HOH B:1731BINDING SITE FOR RESIDUE 4NP B 1701
3AC3SOFTWAREHIS A:549 , PHE A:573 , HOH A:794 , HOH B:1723BINDING SITE FOR RESIDUE GOL A 751

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:416 -A:453
2B:416 -B:453

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Leu A:311 -Pro A:312
2Thr A:358 -Pro A:359
3Gly A:369 -Pro A:370
4Leu B:311 -Pro B:312
5Thr B:358 -Pro B:359
6Gly B:369 -Pro B:370

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VE7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VE7)

(-) Exons   (0, 0)

(no "Exon" information available for 1VE7)

(-) 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:573
 aligned with APEH_AERPE | Q9YBQ2 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:573
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578   
           APEH_AERPE     9 FSRIVRDVERLIAVEKYSLQGVVDGDKLLVVGFSEGSVNAYLYDGGETVKLNREPINSVLDPHYGVGRVILVRDVSKGAEQHALFKVNTSRPGEEQRLEAVKPMRILSGVDTGEAVVFTGATEDRVALYALDGGGLRELARLPGFGFVSDIRGDLIAGLGFFGGGRVSLFTSNLSSGGLRVFDSGEGSFSSASISPGMKVTAGLETAREARLVTVDPRDGSVEDLELPSKDFSSYRPTAITWLGYLPDGRLAVVARREGRSAVFIDGERVEAPQGNHGRVVLWRGKLVTSHTSLSTPPRIVSLPSGEPLLEGGLPEDLRRSIAGSRLVWVESFDGSRVPTYVLESGRAPTPGPTVVLVHGGPFAEDSDSWDTFAASLAAAGFHVVMPNYRGSTGYGEEWRLKIIGDPCGGELEDVSAAARWARESGLASELYIMGYSYGGYMTLCALTMKPGLFKAGVAGASVVDWEEMYELSDAAFRNFIEQLTGGSREIMRSRSPINHVDRIKEPLALIHPQNDSRTPLKPLLRLMGELLARGKTFEAHIIPDAGHAINTMEDAVKILLPAVFFLATQRER 581
               SCOP domains d1ve7a1 A:9-321 Acylamino-acid-releasing enzyme, N-terminal donain                                                                                                                                                                                                                                                       d1ve7a2 A:322-581 Acylamino-acid-releasing enzyme, C-terminal donain                                                                                                                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.eeeeeeee...eeeeeee....eeeeee....eee.......ee.ee.....eeeeeee.......eeeeeee.......ee.......eeeeeee....eeeeee....eeeeeee..eeeeeeee...eeeeeee..eeeeeeeee..eeeeeeee...eeeeee....eeeeeeee.....eeeeeee...eeeeee......eee......hhhhh...eeeeeee.....eeeeeee..eeeeee..eee.....ee...eee..eeeeeeee..eeeeeeee....eee....hhhhhhheeeeeeeeee.....eeeeeeeee......eeeeeee............hhhhhhhhhh..eeeee........hhhhhhh......hhhhhhhhhhhhhhhhh..eeeeeeeeehhhhhhhhhhhhhh.....eeeee....hhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ve7 A   9 FSRIVRDVERLIAVEKYSLQGVVDGDKLLVVGFSEGSVNAYLYDGGETVKLNREPINSVLDPHYGVGRVILVRDVSKGAEQHALFKVNTSRPGEEQRLEAVKPMRILSGVDTGEAVVFTGATEDRVALYALDGGGLRELARLPGFGFVSDIRGDLIAGLGFFGGGRVSLFTSNLSSGGLRVFDSGEGSFSSASISPGMKVTAGLETAREARLVTVDPRDGSVEDLELPSKDFSSYRPTAITWLGYLPDGRLAVVARREGRSAVFIDGERVEAPQGNHGRVVLWRGKLVTSHTSLSTPPRIVSLPSGEPLLEGGLPEDLRRSIAGSRLVWVESFDGSRVPTYVLESGRAPTPGPTVVLVHGGPFAEDSDSWDTFAASLAAAGFHVVMPNYRGSTGYGEEWRLKIIGDPCGGELEDVSAAARWARESGLASELYIMGYSYGGYMTLCALTMKPGLFKAGVAGASVVDWEEMYELSDAAFRNFIEQLTGGSREIMRSRSPINHVDRIKEPLALIHPQNDSRTPLKPLLRLMGELLARGKTFEAHIIPDAGHAINTMEDAVKILLPAVFFLATQRER 581
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578   

Chain B from PDB  Type:PROTEIN  Length:573
 aligned with APEH_AERPE | Q9YBQ2 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:573
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578   
           APEH_AERPE     9 FSRIVRDVERLIAVEKYSLQGVVDGDKLLVVGFSEGSVNAYLYDGGETVKLNREPINSVLDPHYGVGRVILVRDVSKGAEQHALFKVNTSRPGEEQRLEAVKPMRILSGVDTGEAVVFTGATEDRVALYALDGGGLRELARLPGFGFVSDIRGDLIAGLGFFGGGRVSLFTSNLSSGGLRVFDSGEGSFSSASISPGMKVTAGLETAREARLVTVDPRDGSVEDLELPSKDFSSYRPTAITWLGYLPDGRLAVVARREGRSAVFIDGERVEAPQGNHGRVVLWRGKLVTSHTSLSTPPRIVSLPSGEPLLEGGLPEDLRRSIAGSRLVWVESFDGSRVPTYVLESGRAPTPGPTVVLVHGGPFAEDSDSWDTFAASLAAAGFHVVMPNYRGSTGYGEEWRLKIIGDPCGGELEDVSAAARWARESGLASELYIMGYSYGGYMTLCALTMKPGLFKAGVAGASVVDWEEMYELSDAAFRNFIEQLTGGSREIMRSRSPINHVDRIKEPLALIHPQNDSRTPLKPLLRLMGELLARGKTFEAHIIPDAGHAINTMEDAVKILLPAVFFLATQRER 581
               SCOP domains d1ve7b1 B:9-321 Acylamino-acid-releasing enzyme, N-terminal donain                                                                                                                                                                                                                                                       d1ve7b2 B:322-581 Acylamino-acid-releasing enzyme, C-terminal donain                                                                                                                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Peptidase_S9-1ve7B01 B:376-579                                                                                                                                                                              -- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Peptidase_S9-1ve7B02 B:376-579                                                                                                                                                                              -- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhh.eeeeeeee...eeeeeee....eeeeee....eee.......ee.ee.....eeeeeee.......eeeeeee..eeeeeee.......eeeeeee....eeeeeee..eeeeeeee..eeeeeeee...eeeeeee..eeeeeeeee..eeeeeeee...eeeeee....eeeeeeee.....eeeeeee...eeeeee......eee.....hhhhhhh..eeeeeee.....eeeeeee..eeeeee..eee.....ee...ee....eeeeeee..eeeeeeee....eee....hhhhhh.eeeeeeeeee.....eeeeeeeee......eeeeeee............hhhhhhhhhh..eeeee........hhhhhhh......hhhhhhhhhhhhhhhhh..eeeeeeeeehhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ve7 B   9 FSRIVRDVERLIAVEKYSLQGVVDGDKLLVVGFSEGSVNAYLYDGGETVKLNREPINSVLDPHYGVGRVILVRDVSKGAEQHALFKVNTSRPGEEQRLEAVKPMRILSGVDTGEAVVFTGATEDRVALYALDGGGLRELARLPGFGFVSDIRGDLIAGLGFFGGGRVSLFTSNLSSGGLRVFDSGEGSFSSASISPGMKVTAGLETAREARLVTVDPRDGSVEDLELPSKDFSSYRPTAITWLGYLPDGRLAVVARREGRSAVFIDGERVEAPQGNHGRVVLWRGKLVTSHTSLSTPPRIVSLPSGEPLLEGGLPEDLRRSIAGSRLVWVESFDGSRVPTYVLESGRAPTPGPTVVLVHGGPFAEDSDSWDTFAASLAAAGFHVVMPNYRGSTGYGEEWRLKIIGDPCGGELEDVSAAARWARESGLASELYIMGYSYGGYMTLCALTMKPGLFKAGVAGASVVDWEEMYELSDAAFRNFIEQLTGGSREIMRSRSPINHVDRIKEPLALIHPQNDSRTPLKPLLRLMGELLARGKTFEAHIIPDAGHAINTMEDAVKILLPAVFFLATQRER 581
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578   

   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  (2, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1VE7)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (APEH_AERPE | Q9YBQ2)
molecular function
    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:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        APEH_AERPE | Q9YBQ21ve6 2hu5 2hu7 2hu8 2qr5 2qzp 3o4g 3o4h 3o4i 3o4j 4re5 4re6

(-) Related Entries Specified in the PDB File

1ve6 NATIVE ENZYME