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(-) Description

Title :  CRYSTAL STRUCTURE OF THE VMA1-DERIVED ENDONUCLEASE BEARING THE N AND C EXTEIN PROPEPTIDES
 
Authors :  R. Mizutani, Y. Satow
Date :  29 Aug 01  (Deposition) - 29 Aug 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Protein-Splicing, Vma1-Derived Endonuclease, Intein, Thiazolidine Intermediate, Vde, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Mizutani, S. Nogami, M. Kawasaki, Y. Ohya, Y. Anraku, Y. Satow
Protein-Splicing Reaction Via A Thiazolidine Intermediate: Crystal Structure Of The Vma1-Derived Endonuclease Bearing The N And C-Terminal Propeptides.
J. Mol. Biol. V. 316 919 2002
PubMed-ID: 11884132  |  Reference-DOI: 10.1006/JMBI.2001.5357
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VMA1-DERIVED HOMING ENDONUCLEASE X10SSS
    ChainsA, B
    EC Number3.6.1.34
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET-17B-VDE-X10SSS
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 274-747
    GeneVMA1
    MutationYES
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymX10SSS VDE

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1JVA)

(-) Sites  (0, 0)

(no "Site" information available for 1JVA)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JVA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JVA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 6)

Asymmetric Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1INTEIN_N_TERPS50817 Intein N-terminal splicing motif profile.VATA_YEAST284-366
 
  2A:285-366
B:285-366
2INTEIN_ENDONUCLEASEPS50819 Intein DOD-type homing endonuclease domain profile.VATA_YEAST494-642
 
  2A:494-642
B:494-642
3INTEIN_C_TERPS50818 Intein C-terminal splicing motif profile.VATA_YEAST713-738
 
  2A:713-736
B:713-736
Biological Unit 1 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1INTEIN_N_TERPS50817 Intein N-terminal splicing motif profile.VATA_YEAST284-366
 
  1A:285-366
-
2INTEIN_ENDONUCLEASEPS50819 Intein DOD-type homing endonuclease domain profile.VATA_YEAST494-642
 
  1A:494-642
-
3INTEIN_C_TERPS50818 Intein C-terminal splicing motif profile.VATA_YEAST713-738
 
  1A:713-736
-
Biological Unit 2 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1INTEIN_N_TERPS50817 Intein N-terminal splicing motif profile.VATA_YEAST284-366
 
  1-
B:285-366
2INTEIN_ENDONUCLEASEPS50819 Intein DOD-type homing endonuclease domain profile.VATA_YEAST494-642
 
  1-
B:494-642
3INTEIN_C_TERPS50818 Intein C-terminal splicing motif profile.VATA_YEAST713-738
 
  1-
B:713-736

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDL185W1YDL185W.1IV:126788-1300033216VATA_YEAST1-107110712A:282-741 (gaps)
B:279-741 (gaps)
460
463

(-) 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:427
 aligned with VATA_YEAST | P17255 from UniProtKB/Swiss-Prot  Length:1071

    Alignment length:460
                                   291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741
           VATA_YEAST   282 VGCFAKGTNVLMADGSIECIENIEVGNKVMGKDGRPREVIKLPRGRETMYSVVQKSQHRAHKSDSSREVPELLKFTCNATHELVVRTPRSVRRLSRTIKGVEYFEVITFEMGQKKAPDGRIVELVKEVSKSYPISEGPERANELVESYRKASNKAYFEWTIEARDLSLLGSHVRKATYQTYAPILYENDHFFDYMQKSKFHLTIEGPKVLAYLLGLWIGDGLSDRATFSVDSRDTSLMERVTEYAEKLNLCAEYKDRKEPQVAKTVNLYSKVVRGNGIRNNLNTENPLWDAIVGLGFLKDGVKNIPSFLSTDNIGTRETFLAGLIDSDGYVTDEHGIKATIKTIHTSVRDGLVSLARSLGLVVSVNAEPAKVDMNGTKHKISYAIYMSGGDVLLNVLSKCAGSKKFRPAPAAAFARECRGFYFELQELKEDDYYGITLSDDSDHQFLLANQVVVHNCGER 741
               SCOP domains d1jvaa1 A:282-463,A:699-741 VMA1-derived endonuclease (V           DE) PI-Scei intein                                                                                                 d1jvaa2 A:464-581 VMA1-derived endonuclease (VDE) PI-SceI                                                             d1jvaa3 A:582-698 VMA1-derived endonuclease (VDE) PI-SceI                                                            d1jvaa1 A:282-463,A:699-741                 SCOP domains
               CATH domains 1jvaA01 A:282-462,A:699-741 Endonuclease - Pi-scei; Chai           n A, domain 1                                                                                                     ---1jvaA02 A:466-586 Homing endonucleases                                                                                   1jvaA03 A:587-681 Homing endonucleases                                                         -----------------1jvaA01 A:282-462,A:699-741                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...eee.....eee.hhh....eee.....eee.....eeeeeeeeeee..-----------......eeeee...eeeeeee..eeeeeeee..eeeeeeeeeeeeeee.....eeeeeeeeeeeee.hhhhhhhhhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhh.eee.......hhhhhhhhhh......hhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhh..eee.........eeeeeee...------------.hhhhhhhhhh..ee..ee..hhhhhhhhhhhhhhhhhhhhhhheeee.....eeeeee.hhhhhhhhhhhhhhh..eeeeeee.----------..eeeeeee.hhhhhhhhh....................eee.eeeeeeeeeeee..........eee.....eee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --INTEIN_N_TER  PDB: A:285-366 UniProt: 284-366                                      -------------------------------------------------------------------------------------------------------------------------------INTEIN_ENDONUCLEASE  PDB: A:494-642 UniProt: 494-642                                                                                                 ----------------------------------------------------------------------INTEIN_C_TER              --- PROSITE
               Transcript 1 Exon 1.1  PDB: A:282-741 (gaps) UniProt: 1-1071 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                 Transcript 1
                 1jva A 282 VGSFAKGTNVLMADGSIECIENIEVGNKVMGKDGRPREVIKLPRGRETMYSVVQKS-----------EVPELLKFTCNATNELVVRTPRSVRRLSRTIKGVEYFEVITFEMGQKKAPDGRIVELVKEVSKSYPISEGPERANELVESYRKASNKAYFEWTIEARDLSLLGSHVRKATYQTYAPILYENDHFFDYMQKSKFHLTIEGPKVLAYLLGLWIGDGLSDRATFSVDSRDTSLMERVTEYAEKLNLCAEYKDRKEPQVAKTVNLYSKV------------ENPLWDAIVGLGFLKDGVKNIPSFLSTDNIGTRETFLAGLIDSDGYVTDEHGIKATIKTIHTSVRDGLVSLARSLGLVVSVNAEP----------KISYAIYMSGGDVLLNVLSKCAGSKKFRPAPAAAFARECRGFYFELQELKEDDYYGITLSDDSDHQFLLANQVVVHSSGER 741
                                   291       301       311       321       331     |   -       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551 |       -    |  571       581       591       601       611       621       631       641        |-       661       671       681       691       701       711       721       731       741
                                                                                 337         349                                                                                                                                                                                                         553          566                                                                                 650        661                                                                                

Chain B from PDB  Type:PROTEIN  Length:430
 aligned with VATA_YEAST | P17255 from UniProtKB/Swiss-Prot  Length:1071

    Alignment length:463
                                   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       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738   
           VATA_YEAST   279 IIYVGCFAKGTNVLMADGSIECIENIEVGNKVMGKDGRPREVIKLPRGRETMYSVVQKSQHRAHKSDSSREVPELLKFTCNATHELVVRTPRSVRRLSRTIKGVEYFEVITFEMGQKKAPDGRIVELVKEVSKSYPISEGPERANELVESYRKASNKAYFEWTIEARDLSLLGSHVRKATYQTYAPILYENDHFFDYMQKSKFHLTIEGPKVLAYLLGLWIGDGLSDRATFSVDSRDTSLMERVTEYAEKLNLCAEYKDRKEPQVAKTVNLYSKVVRGNGIRNNLNTENPLWDAIVGLGFLKDGVKNIPSFLSTDNIGTRETFLAGLIDSDGYVTDEHGIKATIKTIHTSVRDGLVSLARSLGLVVSVNAEPAKVDMNGTKHKISYAIYMSGGDVLLNVLSKCAGSKKFRPAPAAAFARECRGFYFELQELKEDDYYGITLSDDSDHQFLLANQVVVHNCGER 741
               SCOP domains d1jvab1 B:279-463,B:699-741 VMA1-derived endonuclease (VDE)              PI-Scei intein                                                                                                  d1jvab2 B:464-581 VMA1-derived endonuclease (VDE) PI-SceI                                                             d1jvab3 B:582-698 VMA1-derived endonuclease (VDE) PI-SceI                                                            d1jvab1 B:279-463,B:699-741                 SCOP domains
               CATH domains 1jvaB01 B:279-462,B:699-741 Endonuclease - Pi-scei; Chain A             , domain 1                                                                                                      ---1jvaB02 B:466-586 Homing endonucleases                                                                                   1jvaB03 B:587-681 Homing endonucleases                                                         -----------------1jvaB01 B:279-462,B:699-741                 CATH domains
           Pfam domains (1) -----Hom_end_hint-1jvaB01 B:284-737                                                                                                                                                                                                                                                                                                                                                                                                                                        ---- Pfam domains (1)
           Pfam domains (2) -----Hom_end_hint-1jvaB02 B:284-737                                                                                                                                                                                                                                                                                                                                                                                                                                        ---- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------           ----------------------Hom_end-1jvaB03 B:585-696                                                                                       --------------------------------------------- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------           ----------------------Hom_end-1jvaB04 B:585-696                                                                                       --------------------------------------------- Pfam domains (4)
           Pfam domains (5) -----------------------------------------------------------             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------           ----------------------Hom_end-1jvaB05 B:585-696                                                                                       --------------------------------------------- Pfam domains (5)
           Pfam domains (6) -----------------------------------------------------------             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------           ----------------------Hom_end-1jvaB06 B:585-696                                                                                       --------------------------------------------- Pfam domains (6)
           Pfam domains (7) ATP-synt_ab-1jvaB07 B:279-741                                                                                                                                                                                                                                                                                                                                                                                                                                                   Pfam domains (7)
           Pfam domains (8) ATP-synt_ab-1jvaB08 B:279-741                                                                                                                                                                                                                                                                                                                                                                                                                                                   Pfam domains (8)
         Sec.struct. author ..ee..ee...eee.....eee.hhh....eee.....eeeeee..eeeeeeeeeee..-------------....eeeee...eeeeeee.eeeeeeee....eeeeeeeeeeeeee.....eeeeeeeeeeeee.hhhhhhhhhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhheeee.......hhhhhhhhh.......hhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhh..eeee........eeeeeee.-----------....hhhhhhhhhh..ee..ee...hhhhhhhhhhhhhhhhhhhhhheeee.....eeeeee.hhhhhhhhhhhhhhh..eeeeeee.---------...eeeeeee.hhhhhhhhh....................eee.eeeeeeeeeeee..ee......eee.....eee...ee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----INTEIN_N_TER  PDB: B:285-366 UniProt: 284-366                                      -------------------------------------------------------------------------------------------------------------------------------INTEIN_ENDONUCLEASE  PDB: B:494-642 UniProt: 494-642                                                                                                 ----------------------------------------------------------------------INTEIN_C_TER              --- PROSITE
               Transcript 1 Exon 1.1  PDB: B:279-741 (gaps) UniProt: 1-1071 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                    Transcript 1
                 1jva B 279 IIYVGSFAKGTNVLMADGSIECIENIEVGNKVMGKDGRPREVIKLPRGRETMYSVVQKS-------------PELLKFTCNATNELVVRTPRSVRRLSRTIKGVEYFEVITFEMGQKKAPDGRIVELVKEVSKSYPISEGPERANELVESYRKASNKAYFEWTIEARDLSLLGSHVRKATYQTYAPILYENDHFFDYMQKSKFHLTIEGPKVLAYLLGLWIGDGLSDRATFSVDSRDTSLMERVTEYAEKLNLCAEYKDRKEPQVAKTVNLYS-----------LNTENPLWDAIVGLGFLKDGVKNIPSFLSTDNIGTRETFLAGLIDSDGYVTDEHGIKATIKTIHTSVRDGLVSLARSLGLVVSVNAEP---------HKISYAIYMSGGDVLLNVLSKCAGSKKFRPAPAAAFARECRGFYFELQELKEDDYYGITLSDDSDHQFLLANQVVVHSSGER 741
                                   288       298       308       318       328        |-         -  |    358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548  |      -    |  568       578       588       598       608       618       628       638       648 |       - |     668       678       688       698       708       718       728       738   
                                                                                    337           351                                                                                                                                                                                                     551         563                                                                                    650       660                                                                                 

   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, 6)

Asymmetric Unit

(-) CATH Domains  (2, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (3, 8)

Asymmetric Unit
(-)
Clan: H-int (15)

(-) Gene Ontology  (27, 27)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (VATA_YEAST | P17255)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    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:0016820    hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances    Catalysis of the hydrolysis of an acid anhydride to directly drive the transport of a substance across a membrane.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0046961    proton-transporting ATPase activity, rotational mechanism    Catalysis of the transfer of protons from one side of a membrane to the other according to the reaction: ATP + H2O + H+(in) = ADP + phosphate + H+(out), by a rotational mechanism.
biological process
    GO:0015991    ATP hydrolysis coupled proton transport    The transport of protons against an electrochemical gradient, using energy from ATP hydrolysis.
    GO:0046034    ATP metabolic process    The chemical reactions and pathways involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    GO:0016539    intein-mediated protein splicing    The removal of an internal amino acid sequence (an intein) from a protein during protein maturation; the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues.
    GO:0006314    intron homing    Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0030908    protein splicing    The post-translational removal of peptide sequences from within a protein sequence.
    GO:0015992    proton transport    The directed movement of protons (hydrogen ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0007035    vacuolar acidification    Any process that reduces the pH of the vacuole, measured by the concentration of the hydrogen ion.
cellular component
    GO:0012505    endomembrane system    A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
    GO:0000329    fungal-type vacuole membrane    The lipid bilayer surrounding a vacuole, the shape of which correlates with cell cycle phase. The membrane separates its contents from the cytoplasm of the cell. An example of this structure is found in Saccharomyces cerevisiae.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0033178    proton-transporting two-sector ATPase complex, catalytic domain    A protein complex that forms part of a proton-transporting two-sector ATPase complex and catalyzes ATP hydrolysis or synthesis. The catalytic domain (F1, V1, or A1) comprises a hexameric catalytic core and a central stalk, and is peripherally associated with the membrane when the two-sector ATPase is assembled.
    GO:0005774    vacuolar membrane    The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell.
    GO:0000221    vacuolar proton-transporting V-type ATPase, V1 domain    The V1 domain of a proton-transporting V-type ATPase found in the vacuolar membrane.
    GO:0005773    vacuole    A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

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 Related Entries

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

UniProtKB/Swiss-Prot
        VATA_YEAST | P172551dfa 1ef0 1gpp 1lws 1lwt 1um2 1vde 3j9t 3j9u 3j9v 5bw9 5d80 5vox 5voy 5voz

(-) Related Entries Specified in the PDB File

1ef0 1EF0 CONTAINS PI-SCEI MINIPRECURSOR WITH ZINC ION.
1vde 1VDE CONTAINS PI-SCEI, A HOMING ENDONUCLEASE WITH PROTEIN SPLICING ACTIVITY.