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

(-) Description

Title :  STRUCTURE OF BUB1 KINASE DOMAIN
 
Authors :  Z. H. Lin, L. Y. Jia, D. R. Tomchick, X. L. Luo, H. T. Yu
Date :  24 Jun 14  (Deposition) - 22 Oct 14  (Release) - 24 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Lin, L. Jia, D. R. Tomchick, X. Luo, H. Yu
Substrate-Specific Activation Of The Mitotic Kinase Bub1 Through Intramolecular Autophosphorylation And Kinetochore Targeting.
Structure V. 22 1616 2014
PubMed-ID: 25308863  |  Reference-DOI: 10.1016/J.STR.2014.08.020

(-) Compounds

Molecule 1 - MITOTIC CHECKPOINT SERINE/THREONINE-PROTEIN KINASE BUB1
    Chains: A, B
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Fragment: UNP RESIDUES 749-1094
    Gene: BUB1, BUB1L
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HBUB1, BUB1A

 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  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CL3Ligand/IonCHLORIDE ION
3MG4Ligand/IonMAGNESIUM ION
4SEP2Mod. Amino AcidPHOSPHOSERINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION
4SEP1Mod. Amino AcidPHOSPHOSERINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION
4SEP1Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:794 , GLY A:796 , ALA A:797 , PHE A:798 , ALA A:799 , VAL A:801 , LYS A:821 , MET A:850 , GLU A:867 , TYR A:869 , THR A:873 , ASP A:921 , ASN A:922 , ASP A:946 , MG A:1502 , MG A:1503 , HOH A:1601 , HOH A:1602 , HOH A:1603 , HOH A:1604 , HOH A:1637 , HOH A:1639 , HOH A:1655BINDING SITE FOR RESIDUE ADP A 1501
2AC2SOFTWAREASN A:922 , ASP A:946 , ADP A:1501 , HOH A:1601 , HOH A:1602BINDING SITE FOR RESIDUE MG A 1502
3AC3SOFTWAREASP A:946 , ADP A:1501 , HOH A:1603 , HOH A:1604 , HOH A:1605BINDING SITE FOR RESIDUE MG A 1503
4AC4SOFTWAREGLY B:794 , GLY B:796 , ALA B:797 , PHE B:798 , ALA B:799 , VAL B:801 , LYS B:821 , GLU B:867 , TYR B:869 , THR B:873 , ASP B:921 , ASN B:922 , ILE B:945 , ASP B:946 , MG B:1502 , MG B:1503 , HOH B:1601 , HOH B:1602 , HOH B:1604 , HOH B:1605 , HOH B:1620 , HOH B:1648BINDING SITE FOR RESIDUE ADP B 1501
5AC5SOFTWAREASN B:922 , ASP B:946 , ADP B:1501 , MG B:1503 , HOH B:1601 , HOH B:1602BINDING SITE FOR RESIDUE MG B 1502
6AC6SOFTWAREASP B:946 , ADP B:1501 , MG B:1502 , HOH B:1603 , HOH B:1604 , HOH B:1605BINDING SITE FOR RESIDUE MG B 1503
7AC7SOFTWARELEU B:875 , ASN B:879 , LYS B:882BINDING SITE FOR RESIDUE CL B 1504
8AC8SOFTWAREHOH B:1655BINDING SITE FOR RESIDUE CL B 1505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4QPM)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:824 -Pro A:825
2Lys B:824 -Pro B:825

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4QPM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QPM)

(-) Exons   (0, 0)

(no "Exon" information available for 4QPM)

(-) 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:330
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhh...hhhhh..eee...........eeeee..eeeeeeeeeee...eeeeeee...eeeeeee...hhhhhhhhhhhhhhh...hhhhh..eeeeee....eeeee......hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.hhhhh...eee......ee.hhh..................hhhhh....hhhhhhhhhhhhhhhhhh....eeee..eeee........hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4qpm A  739 PNPWDDKLIFKLLSGLSKPVSSYPNTFEWQCKLPAIKPKTEFQLGSKLVYVHHLLGEGAFAQVYEATQKQKFVLKVQKPANPWEFYIGTQLMERLKPSMQHMFMKFYSAHLFQNGSVLVGELYSYGTLLNAINLYKNTPEKVMPQGLVISFAMRMLYMIEQVHDCEIIHGDIKPDNFILGNGFLESAGLALIDLGQSIDMKLFPKGTIFTAKCETsGFQCVEMLSNKPWNYQIDYFGVAATVYCMLFGTYMKVKNEGGECKPEGLFRRLPHLDMWNEFFHVMLNIPDCHHLPSLDLLRQKLKKVFQQHYTNKIRALRNRLIVLLLECKRS 1083
                                   748       758       768       778       788       798       816       826       836       846       856       866       876       886       896       906       916       926    || 943       953       963     | 973       983       993      1003      1013      1023      1033      1043      1053      1063      1073      1083
                                                                                             806|                                                                                                                 931|                           969-SEP                                                                                                              
                                                                                              815                                                                                                                  939                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:329
                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhh...hhhhh..eee...........eeeee..eeeeeeeeeee...eeeeeee...eeeeee...hhhhhhhhhhhhhhh...hhhhh..eeeeee....eeeee......hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeehhhhhh.....eee......ee.hhh..................hhhhh....hhhhhhhhhhhhhhhhhh....eeee..eeee........hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4qpm B  739 PNPWDDKLIFKLLSGLSKPVSSYPNTFEWQCKLPAIKPKTEFQLGSKLVYVHHLLGEGAFAQVYEATQQKFVLKVQKPANPWEFYIGTQLMERLKPSMQHMFMKFYSAHLFQNGSVLVGELYSYGTLLNAINLYKNTPEKVMPQGLVISFAMRMLYMIEQVHDCEIIHGDIKPDNFILGNGFLEDLSAGLALIDLGQSIDMKLFPKGTIFTAKCETsGFQCVEMLSNKPWNYQIDYFGVAATVYCMLFGTYMKVKNEGGECKPEGLFRRLPHLDMWNEFFHVMLNIPDCHHLPSLDLLRQKLKKVFQQHYTNKIRALRNRLIVLLLECK 1081
                                   748       758       768       778       788       798       817       827       837       847       857       867       877       887       897       907       917       927   ||  942       952       962      |972       982       992      1002      1012      1022      1032      1042      1052      1062      1072         
                                                                                             806|                                                                                                                931|                             969-SEP                                                                                                            
                                                                                              816                                                                                                                 937
   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 4QPM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QPM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QPM)

(-) Gene Ontology  (31, 31)

Asymmetric Unit(hide GO term definitions)

 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
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SEP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:824 - Pro A:825   [ RasMol ]  
    Lys B:824 - Pro B:825   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  4qpm
    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
  BUB1_HUMAN | O43683
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.11.1
    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
  BUB1_HUMAN | O43683
    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
        BUB1_HUMAN | O43683: 2lah 4a1g 4r8q 5dmz

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4QPM)