Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE APEROPYRUM PERNIX RNA SPLICING ENDONUCLEASE
 
Authors :  A. Hirata
Date :  01 Oct 10  (Deposition) - 10 Aug 11  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Biol. Unit 3:  I,J,K,L  (1x)
Keywords :  Mixed Antiparallel And Parallel Beta-Sheet, Heterotetramer, Rna Splicing, Rna, Splicing Endonuclease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Hirata, T. Kitajima, H. Hori
Cleavage Of Intron From The Standard Or Non-Standard Position Of The Precursor Trna By The Splicing Endonuclease Of Aeropyrum Pernix, A Hyper-Thermophilic Crenarchaeon, Involves A Novel Rna Recognition Site In The Crenarchaea Specific Loop
Nucleic Acids Res. V. 39 9376 2011
PubMed-ID: 21846775  |  Reference-DOI: 10.1093/NAR/GKR615

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
    Chains: A, C, E, G, I, K
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSETTA2 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: APE0685
    Organism Scientific: AEROPYRUM PERNIX
    Organism Taxid: 56636
 
Molecule 2 - TRNA-SPLICING ENDONUCLEASE
    Chains: B, D, F, H, J, L
    EC Number: 3.1.27.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSETTA2 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ENDA, APE_1646.1
    Organism Scientific: AEROPYRUM PERNIX
    Organism Taxid: 56636
    Synonym: TRNA-INTRON ENDONUCLEASE

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): ABCD        
Biological Unit 2 (1x):     EFGH    
Biological Unit 3 (1x):         IJKL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3P1Z)

(-) Sites  (0, 0)

(no "Site" information available for 3P1Z)

(-) SS Bonds  (15, 15)

Asymmetric Unit
No.Residues
1A:11 -A:62
2A:27 -A:33
3C:11 -C:62
4C:27 -C:33
5D:5 -D:33
6E:11 -E:62
7E:27 -E:33
8G:11 -G:62
9G:27 -G:33
10H:5 -H:33
11I:11 -I:62
12I:27 -I:33
13K:11 -K:62
14K:27 -K:33
15L:5 -L:33

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Gly B:52 -Pro B:53
2Ile D:8 -Lys D:9
3Gly D:52 -Pro D:53
4Gly F:52 -Pro F:53
5Gly H:52 -Pro H:53
6Gly J:52 -Pro J:53
7Gly L:52 -Pro L:53

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P1Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P1Z)

(-) Exons   (0, 0)

(no "Exon" information available for 3P1Z)

(-) 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:168
 aligned with Q9YE85_AERPE | Q9YE85 from UniProtKB/TrEMBL  Length:170

    Alignment length:168
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162        
         Q9YE85_AERPE     3 KGEGEVAGCKAAARLGVEGVFVEECFDGSYCRNLERIGYLRKGRLEPLEAAYQASRGMLCMGETRGWAAAVEVIAGLGLSLDTALVYFDLRRKGRKPLVGVRRGTLVYEHGGRVYEVLVLSEGYPLKIGSLVEWSRGASMDNHSPIVAIVDRTGLITYYEARAVRSIQ 170
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eeeee..eeeeee..hhhhhhhhhhh..ee..eehhhhhhhhhhh........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...ee.....eeeeee..eeeeeeeee....eehhhhhhhhhhhhhh..eeeeeee.....eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p1z A   3 KGEGEVAGCKAAARLGVEGVFVEECFDGSYCRNLERIGYLRKGRLEPLEAAYQASRGMLCMGETRGWAAAVEVIAGLGLSLDTALVYFDLRRKGRKPLVGVRRGTLVYEHGGRVYEVLVLSEGYPLKIGSLVEWSRGASMDNHSPIVAIVDRTGLITYYEARAVRSIQ 170
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162        


Chain B from PDB  Type:PROTEIN  Length:180
 aligned with ENDA_AERPE | Q9YBF1 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:180
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186
           ENDA_AERPE     7 PIKASGVLIGDSVLVTDVEQARSLYSCGYYGQPLDVEKPRGADFEGPLRLSLIESLYLAEKGVLEVAKPDGSSVGVEDLRTAVRGNPRFSMLYNIYRDLRERGFVVRSGLKFGSDFAVYRLGPGIDHAPFIVHAYSPEDNIDPVEIVRAGRLSHSVRKKFVFAVTRGGDVSYLMIDWFRP 186
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee..eeee.hhhhhhhhhhh....ee..............eeehhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.hhhh..eeee..........eeeeee....ee..hhhhhhhhhh.....eeeeeeee..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p1z B   7 PIKASGVLIGDSVLVTDVEQARSLYSCGYYGQPLDVEKPRGADFEGPLRLSLIESLYLAEKGVLEVAKPDGSSVGVEDLRTAVRGNPRFSMLYNIYRDLRERGFVVRSGLKFGSDFAVYRLGPGIDHAPFIVHAYSPEDNIDPVEIVRAGRLSHSVRKKFVFAVTRGGDVSYLMIDWFRP 186
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186


Chain C from PDB  Type:PROTEIN  Length:161
 aligned with Q9YE85_AERPE | Q9YE85 from UniProtKB/TrEMBL  Length:170

    Alignment length:161
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169 
         Q9YE85_AERPE    10 GCKAAARLGVEGVFVEECFDGSYCRNLERIGYLRKGRLEPLEAAYQASRGMLCMGETRGWAAAVEVIAGLGLSLDTALVYFDLRRKGRKPLVGVRRGTLVYEHGGRVYEVLVLSEGYPLKIGSLVEWSRGASMDNHSPIVAIVDRTGLITYYEARAVRSIQ 170
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....eeeee..hhhhhhhhhhh..ee..eehhhhhhhhhhh..eee..eehhhhhhhhhhhh..hhhhhhhhhhhhhh....ee.....eeeeee..eeeeeeeee....eehhhhhhhhhhhhh...eeeeeee.....eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p1z C  10 GCKAAARLGVEGVFVEECFDGSYCRNLERIGYLRKGRLEPLEAAYQASRGMLCMGETRGWAAAVEVIAGLGLSLDTALVYFDLRRKGRKPLVGVRRGTLVYEHGGRVYEVLVLSEGYPLKIGSLVEWSRGASMDNHSPIVAIVDRTGLITYYEARAVRSIQ 170
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169 


Chain D from PDB  Type:PROTEIN  Length:184
 aligned with ENDA_AERPE | Q9YBF1 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:184
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182    
           ENDA_AERPE     3 DRCAPIKASGVLIGDSVLVTDVEQARSLYSCGYYGQPLDVEKPRGADFEGPLRLSLIESLYLAEKGVLEVAKPDGSSVGVEDLRTAVRGNPRFSMLYNIYRDLRERGFVVRSGLKFGSDFAVYRLGPGIDHAPFIVHAYSPEDNIDPVEIVRAGRLSHSVRKKFVFAVTRGGDVSYLMIDWFRP 186
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee..eeee.hhhhhhhhhhh....ee..............eeeehhhhhhhhhh..eeee.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.hhhh..eeee..........eeeeee....eehhhhhhhhhhhh.....eeeeeeee..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p1z D   3 DRCAPIKASGVLIGDSVLVTDVEQARSLYSCGYYGQPLDVEKPRGADFEGPLRLSLIESLYLAEKGVLEVAKPDGSSVGVEDLRTAVRGNPRFSMLYNIYRDLRERGFVVRSGLKFGSDFAVYRLGPGIDHAPFIVHAYSPEDNIDPVEIVRAGRLSHSVRKKFVFAVTRGGDVSYLMIDWFRP 186
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182    


Chain E from PDB  Type:PROTEIN  Length:168
 aligned with Q9YE85_AERPE | Q9YE85 from UniProtKB/TrEMBL  Length:170

    Alignment length:168
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162        
         Q9YE85_AERPE     3 KGEGEVAGCKAAARLGVEGVFVEECFDGSYCRNLERIGYLRKGRLEPLEAAYQASRGMLCMGETRGWAAAVEVIAGLGLSLDTALVYFDLRRKGRKPLVGVRRGTLVYEHGGRVYEVLVLSEGYPLKIGSLVEWSRGASMDNHSPIVAIVDRTGLITYYEARAVRSIQ 170
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeeee....eeeee..hhhhhhhhhhhh.ee..eehhhhhhhhhhh..eee..ee.hhhhhhhhhhh..hhhhhhhhhhhhhh....ee.....eeeeee..eeeeeeeee....eehhhhhhhhhhhhhh..eeeeeee.....eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p1z E   3 KGEGEVAGCKAAARLGVEGVFVEECFDGSYCRNLERIGYLRKGRLEPLEAAYQASRGMLCMGETRGWAAAVEVIAGLGLSLDTALVYFDLRRKGRKPLVGVRRGTLVYEHGGRVYEVLVLSEGYPLKIGSLVEWSRGASMDNHSPIVAIVDRTGLITYYEARAVRSIQ 170
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162        


Chain F from PDB  Type:PROTEIN  Length:180
 aligned with ENDA_AERPE | Q9YBF1 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:180
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186
           ENDA_AERPE     7 PIKASGVLIGDSVLVTDVEQARSLYSCGYYGQPLDVEKPRGADFEGPLRLSLIESLYLAEKGVLEVAKPDGSSVGVEDLRTAVRGNPRFSMLYNIYRDLRERGFVVRSGLKFGSDFAVYRLGPGIDHAPFIVHAYSPEDNIDPVEIVRAGRLSHSVRKKFVFAVTRGGDVSYLMIDWFRP 186
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee..eeee.hhhhhhhhhhh....ee..............eeeehhhhhhhhhhh.eeee.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee.hhhh..eeee..........eeeeee....ee..hhhhhhhhhh.....eeeeeeee..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p1z F   7 PIKASGVLIGDSVLVTDVEQARSLYSCGYYGQPLDVEKPRGADFEGPLRLSLIESLYLAEKGVLEVAKPDGSSVGVEDLRTAVRGNPRFSMLYNIYRDLRERGFVVRSGLKFGSDFAVYRLGPGIDHAPFIVHAYSPEDNIDPVEIVRAGRLSHSVRKKFVFAVTRGGDVSYLMIDWFRP 186
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186


Chain G from PDB  Type:PROTEIN  Length:161
 aligned with Q9YE85_AERPE | Q9YE85 from UniProtKB/TrEMBL  Length:170

    Alignment length:161
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169 
         Q9YE85_AERPE    10 GCKAAARLGVEGVFVEECFDGSYCRNLERIGYLRKGRLEPLEAAYQASRGMLCMGETRGWAAAVEVIAGLGLSLDTALVYFDLRRKGRKPLVGVRRGTLVYEHGGRVYEVLVLSEGYPLKIGSLVEWSRGASMDNHSPIVAIVDRTGLITYYEARAVRSIQ 170
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....eeeeee.hhhhhhhhhh...ee..eehhhhhhhhhhh...ee....hhhhhhhhhhhhh.hhhhhhhhhhhhhh....ee.....eeeeee..eeeeeeeee....eehhhhhhhhhhhhh...eeeeeee.....eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p1z G  10 GCKAAARLGVEGVFVEECFDGSYCRNLERIGYLRKGRLEPLEAAYQASRGMLCMGETRGWAAAVEVIAGLGLSLDTALVYFDLRRKGRKPLVGVRRGTLVYEHGGRVYEVLVLSEGYPLKIGSLVEWSRGASMDNHSPIVAIVDRTGLITYYEARAVRSIQ 170
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169 


Chain H from PDB  Type:PROTEIN  Length:184
 aligned with ENDA_AERPE | Q9YBF1 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:184
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182    
           ENDA_AERPE     3 DRCAPIKASGVLIGDSVLVTDVEQARSLYSCGYYGQPLDVEKPRGADFEGPLRLSLIESLYLAEKGVLEVAKPDGSSVGVEDLRTAVRGNPRFSMLYNIYRDLRERGFVVRSGLKFGSDFAVYRLGPGIDHAPFIVHAYSPEDNIDPVEIVRAGRLSHSVRKKFVFAVTRGGDVSYLMIDWFRP 186
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee..eeee.hhhhhhhhhh.....ee..............eeeehhhhhhhhhh..eeee.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.hhhh..eeee..........eeeeee....ee.hhhhhhhhhhhh....eeeeeeee..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p1z H   3 DRCAPIKASGVLIGDSVLVTDVEQARSLYSCGYYGQPLDVEKPRGADFEGPLRLSLIESLYLAEKGVLEVAKPDGSSVGVEDLRTAVRGNPRFSMLYNIYRDLRERGFVVRSGLKFGSDFAVYRLGPGIDHAPFIVHAYSPEDNIDPVEIVRAGRLSHSVRKKFVFAVTRGGDVSYLMIDWFRP 186
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182    


Chain I from PDB  Type:PROTEIN  Length:168
 aligned with Q9YE85_AERPE | Q9YE85 from UniProtKB/TrEMBL  Length:170

    Alignment length:168
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162        
         Q9YE85_AERPE     3 KGEGEVAGCKAAARLGVEGVFVEECFDGSYCRNLERIGYLRKGRLEPLEAAYQASRGMLCMGETRGWAAAVEVIAGLGLSLDTALVYFDLRRKGRKPLVGVRRGTLVYEHGGRVYEVLVLSEGYPLKIGSLVEWSRGASMDNHSPIVAIVDRTGLITYYEARAVRSIQ 170
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eeee....eee....hhhhhhhhhhh..ee..eehhhhhhhhhhhh..ee..eehhhhhhhhhhhhh.hhhhhhhhhhhhh.....ee.....eeeee....eeeeeeee....eehhhhhhhhhhhhhh.eeeeeeee.....eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p1z I   3 KGEGEVAGCKAAARLGVEGVFVEECFDGSYCRNLERIGYLRKGRLEPLEAAYQASRGMLCMGETRGWAAAVEVIAGLGLSLDTALVYFDLRRKGRKPLVGVRRGTLVYEHGGRVYEVLVLSEGYPLKIGSLVEWSRGASMDNHSPIVAIVDRTGLITYYEARAVRSIQ 170
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162        


Chain J from PDB  Type:PROTEIN  Length:180
 aligned with ENDA_AERPE | Q9YBF1 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:180
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186
           ENDA_AERPE     7 PIKASGVLIGDSVLVTDVEQARSLYSCGYYGQPLDVEKPRGADFEGPLRLSLIESLYLAEKGVLEVAKPDGSSVGVEDLRTAVRGNPRFSMLYNIYRDLRERGFVVRSGLKFGSDFAVYRLGPGIDHAPFIVHAYSPEDNIDPVEIVRAGRLSHSVRKKFVFAVTRGGDVSYLMIDWFRP 186
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee..eeee.hhhhhhhhhhh....ee..............eeeehhhhhhhhhh..eeee.....eehhhhhhhhhh.hhhhhhhhhhhhhhhh...eeee.hhhh..eeee..........eeeeee....ee..hhhhhhhh.......eeeeee......eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p1z J   7 PIKASGVLIGDSVLVTDVEQARSLYSCGYYGQPLDVEKPRGADFEGPLRLSLIESLYLAEKGVLEVAKPDGSSVGVEDLRTAVRGNPRFSMLYNIYRDLRERGFVVRSGLKFGSDFAVYRLGPGIDHAPFIVHAYSPEDNIDPVEIVRAGRLSHSVRKKFVFAVTRGGDVSYLMIDWFRP 186
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186


Chain K from PDB  Type:PROTEIN  Length:161
 aligned with Q9YE85_AERPE | Q9YE85 from UniProtKB/TrEMBL  Length:170

    Alignment length:161
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169 
         Q9YE85_AERPE    10 GCKAAARLGVEGVFVEECFDGSYCRNLERIGYLRKGRLEPLEAAYQASRGMLCMGETRGWAAAVEVIAGLGLSLDTALVYFDLRRKGRKPLVGVRRGTLVYEHGGRVYEVLVLSEGYPLKIGSLVEWSRGASMDNHSPIVAIVDRTGLITYYEARAVRSIQ 170
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....eeeee..hhhhhhhhh....ee..eehhhhhhhhhhhh..ee....hhhhhhhhhhhh..hhhhhhhhhhhhhh....ee.....eeeee....eeeeeeee....eehhhhhhhhhhhhhh..eeeeeee.....eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p1z K  10 GCKAAARLGVEGVFVEECFDGSYCRNLERIGYLRKGRLEPLEAAYQASRGMLCMGETRGWAAAVEVIAGLGLSLDTALVYFDLRRKGRKPLVGVRRGTLVYEHGGRVYEVLVLSEGYPLKIGSLVEWSRGASMDNHSPIVAIVDRTGLITYYEARAVRSIQ 170
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169 


Chain L from PDB  Type:PROTEIN  Length:184
 aligned with ENDA_AERPE | Q9YBF1 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:184
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182    
           ENDA_AERPE     3 DRCAPIKASGVLIGDSVLVTDVEQARSLYSCGYYGQPLDVEKPRGADFEGPLRLSLIESLYLAEKGVLEVAKPDGSSVGVEDLRTAVRGNPRFSMLYNIYRDLRERGFVVRSGLKFGSDFAVYRLGPGIDHAPFIVHAYSPEDNIDPVEIVRAGRLSHSVRKKFVFAVTRGGDVSYLMIDWFRP 186
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee..eee..hhhhhhhhhhhhh..ee..............ee.hhhhhhhhhhh...eee.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee.hhhh..eeee..........eeeeee....eehhhhhhhhhhhh.....eeeeeeee..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p1z L   3 DRCAPIKASGVLIGDSVLVTDVEQARSLYSCGYYGQPLDVEKPRGADFEGPLRLSLIESLYLAEKGVLEVAKPDGSSVGVEDLRTAVRGNPRFSMLYNIYRDLRERGFVVRSGLKFGSDFAVYRLGPGIDHAPFIVHAYSPEDNIDPVEIVRAGRLSHSVRKKFVFAVTRGGDVSYLMIDWFRP 186
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182
   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 3P1Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P1Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3P1Z)

(-) Gene Ontology  (11, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,C,E,G,I,K   (Q9YE85_AERPE | Q9YE85)
molecular function
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000213    tRNA-intron endonuclease activity    Catalysis of the endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxyl and 2',3'-cyclic phosphate termini, and specifically removing the intron.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0006388    tRNA splicing, via endonucleolytic cleavage and ligation    Splicing of tRNA substrates via recognition of the folded RNA structure that brings the 5' and 3' splice sites into proximity and cleavage of the RNA at both the 3' and 5' splice sites by an endonucleolytic mechanism, followed by ligation of the exons.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain B,D,F,H,J,L   (ENDA_AERPE | Q9YBF1)
molecular function
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000213    tRNA-intron endonuclease activity    Catalysis of the endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxyl and 2',3'-cyclic phosphate termini, and specifically removing the intron.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
    GO:0006388    tRNA splicing, via endonucleolytic cleavage and ligation    Splicing of tRNA substrates via recognition of the folded RNA structure that brings the 5' and 3' splice sites into proximity and cleavage of the RNA at both the 3' and 5' splice sites by an endonucleolytic mechanism, followed by ligation of the exons.

 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
(no "Ligands, Modified Residues, Ions" information available for 3p1z)
 
  Sites
(no "Sites" information available for 3p1z)
 
  Cis Peptide Bonds
    Gly B:52 - Pro B:53   [ RasMol ]  
    Gly D:52 - Pro D:53   [ RasMol ]  
    Gly F:52 - Pro F:53   [ RasMol ]  
    Gly H:52 - Pro H:53   [ RasMol ]  
    Gly J:52 - Pro J:53   [ RasMol ]  
    Gly L:52 - Pro L:53   [ RasMol ]  
    Ile D:8 - Lys D:9   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 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
  3p1z
    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
  ENDA_AERPE | Q9YBF1
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  Q9YE85_AERPE | Q9YE85
    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)
  3.1.27.9
    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
  ENDA_AERPE | Q9YBF1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q9YE85_AERPE | Q9YE85
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ENDA_AERPE | Q9YBF1: 3ajv 3p1y
UniProtKB/TrEMBL
        Q9YE85_AERPE | Q9YE85: 3ajv

(-) Related Entries Specified in the PDB File

3p1y