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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN BRAIN-TYPE CREATINE KINASE
 
Authors :  S. M. Bong, J. H. Moon, K. Y. Hwang
Date :  29 Oct 07  (Deposition) - 04 Nov 08  (Release) - 17 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Brain Type, Dimeric, , Atp-Binding, Cytoplasm, Kinase, Nucleotide-Binding, Phosphorylation, Polymorphism, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. M. Bong, J. H. Moon, K. H. Nam, K. S. Lee, Y. M. Chi, K. Y. Hwang
Structural Studies Of Human Brain-Type Creatine Kinase Complexed With The Adp-Mg2+-No3- -Creatine Transition-State Analogue Complex
Febs Lett. V. 582 3959 2008
PubMed-ID: 18977227  |  Reference-DOI: 10.1016/J.FEBSLET.2008.10.039
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CREATINE KINASE B-TYPE
    ChainsA, B
    EC Number2.7.3.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneCKB
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCREATINE KINASE B CHAIN, B-CK

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric/Biological Unit (5, 6)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
3CRN1Ligand/IonN-[(E)-AMINO(IMINO)METHYL]-N-METHYLGLYCINE
4MG1Ligand/IonMAGNESIUM ION
5NO31Ligand/IonNITRATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREADP B:601 , NO3 B:602 , HOH B:979BINDING SITE FOR RESIDUE MG B 600
2AC2SOFTWAREARG B:132 , GLU B:232 , ARG B:236 , ARG B:320 , MG B:600 , ADP B:601 , CRN B:603 , HOH B:795 , HOH B:979BINDING SITE FOR RESIDUE NO3 B 602
3AC3SOFTWAREPRO A:200 , ASP B:268 , HOH B:964BINDING SITE FOR RESIDUE ACT B 604
4AC4SOFTWAREASN A:222 , LYS A:223 , THR A:224 , LYS A:242 , HOH A:945BINDING SITE FOR RESIDUE ACT A 605
5AC5SOFTWARESER B:128 , ARG B:130 , ARG B:132 , HIS B:191 , ARG B:292 , GLY B:294 , VAL B:295 , HIS B:296 , ARG B:320 , THR B:322 , GLY B:323 , GLY B:324 , VAL B:325 , ASP B:335 , MG B:600 , NO3 B:602 , HOH B:773 , HOH B:775 , HOH B:804 , HOH B:819 , HOH B:935BINDING SITE FOR RESIDUE ADP B 601
6AC6SOFTWARETHR B:71 , VAL B:72 , LEU B:201 , GLU B:232 , CYS B:283 , SER B:285 , NO3 B:602 , HOH B:780 , HOH B:792 , HOH B:801 , HOH B:934 , HOH B:974BINDING SITE FOR RESIDUE CRN B 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3B6R)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:211 -Pro A:212
2Trp B:211 -Pro B:212

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric/Biological Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_025838K177RKCRB_HUMANPolymorphism36002620A/BK177R
2UniProtVAR_025839S309LKCRB_HUMANPolymorphism35156510A/BS309L
3UniProtVAR_049674L360FKCRB_HUMANPolymorphism12505A/BL360F

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PHOSPHAGEN_KINASE_NPS51509 Phosphagen kinase N-terminal domain profile.KCRB_HUMAN11-98
 
  2A:11-98
B:11-98
2PHOSPHAGEN_KINASE_CPS51510 Phosphagen kinase C-terminal domain profile.KCRB_HUMAN125-367
 
  2A:125-367
B:125-367
3PHOSPHAGEN_KINASEPS00112 Phosphagen kinase active site signature.KCRB_HUMAN283-289
 
  2A:283-289
B:283-289

(-) Exons   (0, 0)

(no "Exon" information available for 3B6R)

(-) Sequences/Alignments

Asymmetric/Biological 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:376
 aligned with KCRB_HUMAN | P12277 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:376
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375      
           KCRB_HUMAN     6 SHNALKLRFPAEDEFPDLSAHNNHMAKVLTPELYAELRAKSTPSGFTLDDVIQTGVDNPGHPYIMTVGCVAGDEESYEVFKDLFDPIIEDRHGGYKPSDEHKTDLNPDNLQGGDDLDPNYVLSSRVRTGRSIRGFCLPPHCSRGERRAIEKLAVEALSSLDGDLAGRYYALKSMTEAEQQQLIDDHFLFDKPVSPLLLASGMARDWPDARGIWHNDNKTFLVWVNEEDHLRVISMQKGGNMKEVFTRFCTGLTQIETLFKSKDYEFMWNPHLGYILTCPSNLGTGLRAGVHIKLPNLGKHEKFSEVLKRLRLQKRGTGGVDTAAVGGVFDVSNADRLGFSEVELVQMVVDGVKLLIEMEQRLEQGQAIDDLMPAQK 381
               SCOP domains d3b6ra1 A:6-102 automated matches                                                                d3b6ra2 A:103-381 automated matches                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 3b6rA01 A:6-102 Transferase Creatine Kinase, Chain A, domain 1                                   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh..hhhhhh.......hhhhhhhhhhhhhhhh........hhhhhhhhhhhh................hhhhhhhhhhhhhhhhhh.............hhhhh..........eeeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhh........hhhhhh...........eeeee....eeeee.....eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhh.....ee...ee...hhhhh....eeeeeeehhhhhh..hhhhhhhhh.eeeee..hhhhhhhh.eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------R-----------------------------------------------------------------------------------------------------------------------------------L--------------------------------------------------F--------------------- SAPs(SNPs)
                PROSITE (1) -----PHOSPHAGEN_KINASE_N  PDB: A:11-98 UniProt: 11-98                                        --------------------------PHOSPHAGEN_KINASE_C  PDB: A:125-367 UniProt: 125-367                                                                                                                                                                                               -------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PHOSPHA-------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b6r A   6 SHNALKLRFPAEDEFPDLSAHNNHMAKVLTPELYAELRAKSTPSGFTLDDVIQTGVDNPGHPYIMTVGCVAGDEESYEVFKDLFDPIIEDRHGGYKPSDEHKTDLNPDNLQGGDDLDPNYVLSSRVRTGRSIRGFCLPPHCSRGERRAIEKLAVEALSSLDGDLAGRYYALKSMTEAEQQQLIDDHFLFDKPVSPLLLASGMARDWPDARGIWHNDNKTFLVWVNEEDHLRVISMQKGGNMKEVFTRFCTGLTQIETLFKSKDYEFMWNPHLGYILTCPSNLGTGLRAGVHIKLPNLGKHEKFSEVLKRLRLQKRGTGGVDTAAVGGVFDVSNADRLGFSEVELVQMVVDGVKLLIEMEQRLEQGQAIDDLMPAQK 381
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375      

Chain B from PDB  Type:PROTEIN  Length:376
 aligned with KCRB_HUMAN | P12277 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:376
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375      
           KCRB_HUMAN     6 SHNALKLRFPAEDEFPDLSAHNNHMAKVLTPELYAELRAKSTPSGFTLDDVIQTGVDNPGHPYIMTVGCVAGDEESYEVFKDLFDPIIEDRHGGYKPSDEHKTDLNPDNLQGGDDLDPNYVLSSRVRTGRSIRGFCLPPHCSRGERRAIEKLAVEALSSLDGDLAGRYYALKSMTEAEQQQLIDDHFLFDKPVSPLLLASGMARDWPDARGIWHNDNKTFLVWVNEEDHLRVISMQKGGNMKEVFTRFCTGLTQIETLFKSKDYEFMWNPHLGYILTCPSNLGTGLRAGVHIKLPNLGKHEKFSEVLKRLRLQKRGTGGVDTAAVGGVFDVSNADRLGFSEVELVQMVVDGVKLLIEMEQRLEQGQAIDDLMPAQK 381
               SCOP domains d3b6rb1 B:6-102 automated matches                                                                d3b6rb2 B:103-381 automated matches                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 3b6rB01 B:6-102 Transferase Creatine Kinase, Chain A, domain 1                                   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh..hhhhhh.......hhhhhhhhhhhhhhhh........hhhhhhhhhhhh................hhhhhhhhhhhhhhhhhh.............hhhhh..........eeeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhh........hhhhhhh..........eeeee....eeeee.....eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhh.....ee...ee...hhhhh....eeeeeeehhhhhh..hhhhhhhhh.eeee............eeeeee......hhhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------R-----------------------------------------------------------------------------------------------------------------------------------L--------------------------------------------------F--------------------- SAPs(SNPs)
                PROSITE (1) -----PHOSPHAGEN_KINASE_N  PDB: B:11-98 UniProt: 11-98                                        --------------------------PHOSPHAGEN_KINASE_C  PDB: B:125-367 UniProt: 125-367                                                                                                                                                                                               -------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PHOSPHA-------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b6r B   6 SHNALKLRFPAEDEFPDLSAHNNHMAKVLTPELYAELRAKSTPSGFTLDDVIQTGVDNPGHPYIMTVGCVAGDEESYEVFKDLFDPIIEDRHGGYKPSDEHKTDLNPDNLQGGDDLDPNYVLSSRVRTGRSIRGFCLPPHCSRGERRAIEKLAVEALSSLDGDLAGRYYALKSMTEAEQQQLIDDHFLFDKPVSPLLLASGMARDWPDARGIWHNDNKTFLVWVNEEDHLRVISMQKGGNMKEVFTRFCTGLTQIETLFKSKDYEFMWNPHLGYILTCPSNLGTGLRAGVHIKLPNLGKHEKFSEVLKRLRLQKRGTGGVDTAAVGGVFDVSNADRLGFSEVELVQMVVDGVKLLIEMEQRLEQGQAIDDLMPAQK 381
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375      

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3B6R)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (KCRB_HUMAN | P12277)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004111    creatine kinase activity    Catalysis of the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+).
    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: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.
    GO:0016772    transferase activity, transferring phosphorus-containing groups    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0007420    brain development    The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    GO:0030644    cellular chloride ion homeostasis    Any process involved in the maintenance of an internal steady state of chloride ions at the level of a cell.
    GO:0006600    creatine metabolic process    The chemical reactions and pathways involving creatine (N-(aminoiminomethyl)-N-methylglycine), a compound synthesized from the amino acids arginine, glycine, and methionine that occurs in muscle.
    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:0021762    substantia nigra development    The progression of the substantia nigra over time from its initial formation until its mature state. The substantia nigra is the layer of gray substance that separates the posterior parts of the cerebral peduncles (tegmentum mesencephali) from the anterior parts; it normally includes a posterior compact part with many pigmented cells (pars compacta) and an anterior reticular part whose cells contain little pigment (pars reticularis).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0043209    myelin sheath    An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.

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 Related Entries

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

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        KCRB_HUMAN | P122773drb 3dre

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