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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CONSERVED N-TERMINAL DOMAIN OF THE MITOTIC CHECKPOINT COMPONENT BUB1
 
Authors :  V. M. Bolanos-Garcia, D. Y. Chirgadze, T. L. Blundell
Date :  06 Oct 08  (Deposition) - 17 Feb 09  (Release) - 17 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.74
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Bub1, Mitotic Spindle Checkpoint, Tpr Motif, All-Alpha Domain, Mad3-Like Domain, Chromosome Instability, Atp- Binding, Cell Cycle, Kinase, Nucleotide-Binding, Nucleus, Phosphorylation, Serine/Threonine-Protein Kinase, Transferase, Kinetochore Localization, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. M. Bolanos-Garcia, T. Kiyomitsu, S. D'Arcy, D. Y. Chirgadze, J. G. Grossmann, D. Matak-Vinkovic, A. R. Venkitaraman, M. Yanagida, C. V. Robinson, T. L. Blundell
The Crystal Structure Of The N-Terminal Region Of Bub1 Provides Insight Into The Mechanism Of Bub1 Recruitment To Kinetochores.
Structure V. 17 105 2009
PubMed-ID: 19141287  |  Reference-DOI: 10.1016/J.STR.2008.10.015
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHECKPOINT SERINE/THREONINE-PROTEIN KINASE BUB1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCONSERVED N-TERMINAL DOMAIN (RESIDUES 29-230)
    GeneBUB1, G7542, YGR188C
    Organism CommonBREWER'S YEAST,LAGER BEER YEAST,YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    StrainYJM789

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NHE2Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NHE1Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NHE1Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:113BINDING SITE FOR RESIDUE NHE A 520
2AC2SOFTWAREILE B:66 , TRP B:113 , ASN B:116 , LEU B:117 , HOH B:650BINDING SITE FOR RESIDUE NHE B 510

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Arg A:175 -Pro A:176
2Arg B:175 -Pro B:176
3Val B:203 -Pro B:204

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BUB1_NPS51489 BUB1 N-terminal domain profile.BUB1_YEAST47-212
 
  2A:47-212
B:47-212
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BUB1_NPS51489 BUB1 N-terminal domain profile.BUB1_YEAST47-212
 
  1A:47-212
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BUB1_NPS51489 BUB1 N-terminal domain profile.BUB1_YEAST47-212
 
  1-
B:47-212

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YGR188C1YGR188C.1VII:875114-8720493066BUB1_YEAST1-102110212A:31-229 (gaps)
B:29-230
199
202

(-) 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:195
 aligned with A6ZUJ9_YEAS7 | A6ZUJ9 from UniProtKB/TrEMBL  Length:1021

    Alignment length:199
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220         
         A6ZUJ9_YEAS7    31 EQHSQLNQTKIAYEQRLLNDLEDMDDPLDLFLDYMIWISTSYIEVDSESGQEVLRSTMERCLIYIQDMETYRNDPRFLKIWIWYINLFLSNNFHESENTFKYMFNKGIGTKLSLFYEEFSKLLENAQFFLEAKVLLELGAENNCRPYNRLLRSLSNYEDRLREMNIVENQNSVPDSRERLKGRLNYRTAPFFIRKFLTS 229
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....----hhhhhhhhhhhh....hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3esl A  31 EQHSQLNQTKIAYEQRLLNDLEDMDDPLDLFLDYMIWISTSYIEVDSESGQEVLRSTMERCLIYIQDMETYRNDPRFLKIWIWYINLFLSNNFHESENTFKYMFNKGIGTKLSLFYEEFSKLLENAQFFLEAKVLLELGAENNCRPYNRLLRSLSNYEDRLREMNIVEN----PDSRERLKGRLIYRTAPFFIRKFLTS 229
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190        |-   |   210       220         
                                                                                                                                                                                                  199  204                         

Chain A from PDB  Type:PROTEIN  Length:195
 aligned with BUB1_YEAST | P41695 from UniProtKB/Swiss-Prot  Length:1021

    Alignment length:199
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220         
           BUB1_YEAST    31 EQHSQLNQTKIAYEQRLLNDLEDMDDPLDLFLDYMIWISTSYIEVDSESGQEVLRSTMERCLIYIQDMETYRNDPRFLKIWIWYINLFLSNNFHESENTFKYMFNKGIGTKLSLFYEEFSKLLENAQFFLEAKVLLELGAENNCRPYNRLLRSLSNYEDRLREMNIVENQNSVPDSRERLKGRLIYRTAPFFIRKFLTS 229
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....----hhhhhhhhhhhh....hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------BUB1_N  PDB: A:47-212 UniProt: 47-212                                                                                                                                 ----------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:31-229 (gaps) UniProt: 1-1021 [INCOMPLETE]                                                                                                                                             Transcript 1
                 3esl A  31 EQHSQLNQTKIAYEQRLLNDLEDMDDPLDLFLDYMIWISTSYIEVDSESGQEVLRSTMERCLIYIQDMETYRNDPRFLKIWIWYINLFLSNNFHESENTFKYMFNKGIGTKLSLFYEEFSKLLENAQFFLEAKVLLELGAENNCRPYNRLLRSLSNYEDRLREMNIVEN----PDSRERLKGRLIYRTAPFFIRKFLTS 229
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190        |-   |   210       220         
                                                                                                                                                                                                  199  204                         

Chain B from PDB  Type:PROTEIN  Length:202
 aligned with A6ZUJ9_YEAS7 | A6ZUJ9 from UniProtKB/TrEMBL  Length:1021

    Alignment length:202
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228  
         A6ZUJ9_YEAS7    29 QKEQHSQLNQTKIAYEQRLLNDLEDMDDPLDLFLDYMIWISTSYIEVDSESGQEVLRSTMERCLIYIQDMETYRNDPRFLKIWIWYINLFLSNNFHESENTFKYMFNKGIGTKLSLFYEEFSKLLENAQFFLEAKVLLELGAENNCRPYNRLLRSLSNYEDRLREMNIVENQNSVPDSRERLKGRLNYRTAPFFIRKFLTSS 230
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhh....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3esl B  29 QKEQHSQLNQTKIAYEQRLLNDLEDMDDPLDLFLDYMIWISTSYIEVDSESGQEVLRSTMERCLIYIQDMETYRNDPRFLKIWIWYINLFLSNNFHESENTFKYMFNKGIGTKLSLFYEEFSKLLENAQFFLEAKVLLELGAENNCRPYNRLLRSLSNYEDRLREMNIVENQNSVPDSRERLKGRLIYRTAPFFIRKFLTSS 230
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228  

Chain B from PDB  Type:PROTEIN  Length:202
 aligned with BUB1_YEAST | P41695 from UniProtKB/Swiss-Prot  Length:1021

    Alignment length:202
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228  
           BUB1_YEAST    29 QKEQHSQLNQTKIAYEQRLLNDLEDMDDPLDLFLDYMIWISTSYIEVDSESGQEVLRSTMERCLIYIQDMETYRNDPRFLKIWIWYINLFLSNNFHESENTFKYMFNKGIGTKLSLFYEEFSKLLENAQFFLEAKVLLELGAENNCRPYNRLLRSLSNYEDRLREMNIVENQNSVPDSRERLKGRLIYRTAPFFIRKFLTSS 230
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhh....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------BUB1_N  PDB: B:47-212 UniProt: 47-212                                                                                                                                 ------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: B:29-230 UniProt: 1-1021 [INCOMPLETE]                                                                                                                                                       Transcript 1
                 3esl B  29 QKEQHSQLNQTKIAYEQRLLNDLEDMDDPLDLFLDYMIWISTSYIEVDSESGQEVLRSTMERCLIYIQDMETYRNDPRFLKIWIWYINLFLSNNFHESENTFKYMFNKGIGTKLSLFYEEFSKLLENAQFFLEAKVLLELGAENNCRPYNRLLRSLSNYEDRLREMNIVENQNSVPDSRERLKGRLIYRTAPFFIRKFLTSS 230
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228  

   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 3ESL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (BUB1_YEAST | P41695)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0034508    centromere complex assembly    The aggregation, arrangement and bonding together of proteins and centromeric DNA molecules to form a centromeric protein-DNA complex. Includes the formation of the chromatin structures which form a platform for the kinetochore, and assembly of the kinetochore onto this specialized chromatin. In fission yeast and higher eukaryotes this process also includes the formation of heterochromatin at the outer repeat (pericentric) regions of the centromere.
    GO:0016236    macroautophagy    The major inducible pathway for the general turnover of cytoplasmic constituents in eukaryotic cells, it is also responsible for the degradation of active cytoplasmic enzymes and organelles during nutrient starvation. Macroautophagy involves the formation of double-membrane-bounded autophagosomes which enclose the cytoplasmic constituent targeted for degradation in a membrane-bounded structure. Autophagosomes then fuse with a lysosome (or vacuole) releasing single-membrane-bounded autophagic bodies that are then degraded within the lysosome (or vacuole). Though once thought to be a purely non-selective process, it appears that some types of macroautophagy, e.g. macropexophagy, macromitophagy, may involve selective targeting of the targets to be degraded.
    GO:0007094    mitotic spindle assembly checkpoint    A cell cycle checkpoint that delays the metaphase/anaphase transition of a mitotic nuclear division until the spindle is correctly assembled and chromosomes are attached to the spindle.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0034501    protein localization to kinetochore    Any process in which a protein is transported to, or maintained at, the kinetochore.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0031134    sister chromatid biorientation    The cell cycle process in which sister chromatids establish stable attachments to microtubules emanating from opposite spindle poles.
cellular component
    GO:0000778    condensed nuclear chromosome kinetochore    A multisubunit complex that is located at the centromeric region of a condensed nuclear chromosome and provides an attachment point for the spindle microtubules.
    GO:0000780    condensed nuclear chromosome, centromeric region    The region of a condensed nuclear chromosome that includes the centromere and associated proteins, including the kinetochore. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
    GO:0000776    kinetochore    A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Chain A,B   (A6ZUJ9_YEAS7 | A6ZUJ9)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
biological process
    GO:0007094    mitotic spindle assembly checkpoint    A cell cycle checkpoint that delays the metaphase/anaphase transition of a mitotic nuclear division until the spindle is correctly assembled and chromosomes are attached to the spindle.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BUB1_YEAST | P416952i3s 4bl0

(-) Related Entries Specified in the PDB File

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