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(-) Description

Title :  CRYSTAL STRUCTURE OF THE KIF2C MOTOR DOMAIN (CASP TARGET)
 
Authors :  J. Wang, Y. Shen, W. Tempel, R. Landry, C. H. Arrowsmith, A. M. Edwards, M. Sundstrom, J. Weigelt, A. Bochkarev, H. Park, Structural Genomics Consortium (Sgc)
Date :  21 Jun 06  (Deposition) - 18 Jul 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A
Keywords :  Kinesin, Motor Domain, Adp, Structural Genomics, Structural Genomics Consortium, Sgc, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Wang, Y. Shen, W. Tempel, R. Landry, C. H. Arrowsmith, A. M. Edwards, M. Sundstrom, J. Weigelt, A. Bochkarev, H. Park
Crystal Structure Of The Kif2C Motor Domain
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KIF2C PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidP28A-LIC
    Expression System StrainBL21-CODONPLUS (DE-3)-RIL
    Expression System Taxid562
    GeneKIF2C
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymKINESIN-LIKE 6, MITOTIC CENTROMERE-ASSOCIATED KINESIN, KINESIN FAMILY MEMBER 2C

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3UNX10Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:355 , ADP A:601 , HOH A:704 , HOH A:705 , HOH A:706 , HOH A:707BINDING SITE FOR RESIDUE MG A 602
02AC2SOFTWAREARG A:264 , ARG A:266 , PRO A:267 , GLN A:349 , THR A:350 , GLY A:351 , SER A:352 , GLY A:353 , LYS A:354 , THR A:355 , HIS A:356 , MG A:602 , HOH A:705 , HOH A:706 , HOH A:707 , HOH A:718 , HOH A:719 , HOH A:733BINDING SITE FOR RESIDUE ADP A 601
03AC3SOFTWAREVAL A:421 , LYS A:543BINDING SITE FOR RESIDUE UNX A 801
04AC4SOFTWAREILE A:404 , SER A:519 , LYS A:543 , LEU A:544BINDING SITE FOR RESIDUE UNX A 802
05AC5SOFTWARELYS A:297BINDING SITE FOR RESIDUE UNX A 803
06AC6SOFTWAREGLU A:305 , ASN A:306 , GLN A:307 , ARG A:580BINDING SITE FOR RESIDUE UNX A 804
07AC7SOFTWAREGLU A:436 , MET A:484 , LYS A:487BINDING SITE FOR RESIDUE UNX A 805
08AC8SOFTWAREASP A:424BINDING SITE FOR RESIDUE UNX A 806
09AC9SOFTWAREILE A:259BINDING SITE FOR RESIDUE UNX A 807
10BC1SOFTWAREMET A:358 , GLY A:359 , GLY A:372 , TYR A:374 , ALA A:375BINDING SITE FOR RESIDUE UNX A 808
11BC2SOFTWARELEU A:384BINDING SITE FOR RESIDUE UNX A 809
12BC3SOFTWAREGLN A:427 , HIS A:536 , THR A:537 , PHE A:539 , ARG A:549 , HOH A:709BINDING SITE FOR RESIDUE UNX A 810

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:344 -A:560

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2HEH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049683I449LKIF2C_HUMANPolymorphism4342887AI449L

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KINESIN_MOTOR_2PS50067 Kinesin motor domain profile.KIF2C_HUMAN258-588  1A:258-587
2KINESIN_MOTOR_1PS00411 Kinesin motor domain signature.KIF2C_HUMAN486-497  1A:486-497

(-) Exons   (11, 11)

Asymmetric/Biological Unit (11, 11)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003722241bENSE00001945221chr1:45205492-45205674183KIF2C_HUMAN1-24240--
1.2ENST000003722242ENSE00001734334chr1:45206585-4520667995KIF2C_HUMAN24-55320--
1.4ENST000003722244ENSE00001752907chr1:45213056-45213157102KIF2C_HUMAN56-89340--
1.5ENST000003722245ENSE00001769500chr1:45213324-4521337249KIF2C_HUMAN90-106170--
1.6bENST000003722246bENSE00001627695chr1:45216114-45216236123KIF2C_HUMAN106-147420--
1.7bENST000003722247bENSE00001631477chr1:45218804-45218926123KIF2C_HUMAN147-188420--
1.8ENST000003722248ENSE00001659028chr1:45219405-45219505101KIF2C_HUMAN188-221340--
1.9ENST000003722249ENSE00001734027chr1:45220422-4522051796KIF2C_HUMAN222-253321A:229-25325
1.10ENST0000037222410ENSE00001652465chr1:45221601-4522165555KIF2C_HUMAN254-272191A:254-27219
1.11cENST0000037222411cENSE00002151499chr1:45221747-45221909163KIF2C_HUMAN272-326551A:272-32655
1.12ENST0000037222412ENSE00001631000chr1:45223228-4522331891KIF2C_HUMAN326-356311A:326-35631
1.13bENST0000037222413bENSE00002181680chr1:45223580-4522364364KIF2C_HUMAN357-378221A:357-378 (gaps)22
1.14ENST0000037222414ENSE00001678770chr1:45223721-4522381292KIF2C_HUMAN378-408311A:378-40831
1.15ENST0000037222415ENSE00001689958chr1:45224878-45225020143KIF2C_HUMAN409-456481A:409-45648
1.16aENST0000037222416aENSE00001770471chr1:45225952-45226156205KIF2C_HUMAN456-524691A:456-524 (gaps)69
1.17ENST0000037222417ENSE00001712066chr1:45226264-45226374111KIF2C_HUMAN525-561371A:525-56137
1.18ENST0000037222418ENSE00001662209chr1:45227588-4522765568KIF2C_HUMAN562-584231A:562-58423
1.19cENST0000037222419cENSE00001747875chr1:45228018-45228123106KIF2C_HUMAN584-619361A:584-5874
1.20bENST0000037222420bENSE00001685683chr1:45228217-45228330114KIF2C_HUMAN620-657380--
1.21bENST0000037222421bENSE00001726373chr1:45232498-45232621124KIF2C_HUMAN658-699420--
1.22bENST0000037222422bENSE00001457243chr1:45232769-45233439671KIF2C_HUMAN699-725270--

(-) 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:324
 aligned with KIF2C_HUMAN | Q99661 from UniProtKB/Swiss-Prot  Length:725

    Alignment length:359
                                   238       248       258       268       278       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         
          KIF2C_HUMAN   229 NWEFARMIKEFRATLECHPLTMTDPIEEHRICVCVRKRPLNKQELAKKEIDVISIPSKCLLLVHEPKLKVDLTKYLENQAFCFDFAFDETASNEVVYRFTARPLVQTIFEGGKATCFAYGQTGSGKTHTMGGDLSGKAQNASKGIYAMASRDVFLLKNQPCYRKLGLEVYVTFFEIYNGKLFDLLNKKAKLRVLEDGKQQVQVVGLQEHLVNSADDVIKMIDMGSACRTSGQTFANSNSSRSHACFQIILRAKGRMHGKFSLVDLAGNERGADTSSADRQTRMEGAEINKSLLALKECIRALGQNKAHTPFRESKLTQVLRDSFIGENSRTCMIATISPGISSCEYTLNTLRYADRVKE 587
               SCOP domains d2heha_ A: Kinesin                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2hehA00 A:229-587 Kinesin                                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh...............eeeeeee...hhhhhhh.....ee.....eeeeeeeee.....eeeeeeeee..eee....hhhhhhhhhhhhhhhhhhh..eeeeeee.....hhhhhhh-----------.hhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee..eeee.....ee.eeee.....eeee....eee.hhhhhhhhhhhhhhhh---------hhhhheeeeeeeee....eeeeeeeee.....---------------hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...eeeeeeeee..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----------------------------KINESIN_MOTOR_2  PDB: A:258-587 UniProt: 258-588                                                                                                                                                                                                                                                                                           PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KINESIN_MOTO------------------------------------------------------------------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.9  PDB: A:229-253 Exon 1.10          -----------------------------------------------------Exon 1.12  PDB: A:326-356      Exon 1.13b            ------------------------------Exon 1.15  PDB: A:409-456 UniProt: 409-456      --------------------------------------------------------------------Exon 1.17  PDB: A:525-561            Exon 1.18              --- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.11c  PDB: A:272-326 UniProt: 272-326            ---------------------------------------------------Exon 1.14  PDB: A:378-408      -----------------------------------------------Exon 1.16a  PDB: A:456-524 (gaps) UniProt: 456-524                   -----------------------------------------------------------1.19 Transcript 1 (2)
                 2heh A 229 NWEFARMIKEFRATLECHPLTMTDPIEEHRICVCVRKRPLNKQELAKKEIDVISIPSKCLLLVHEPKLKVDLTKYLENQAFCFDFAFDETASNEVVYRFTARPLVQTIFEGGKATCFAYGQTGSGKTHTMG-----------KGIYAMASRDVFLLKNQPCYRKLGLEVYVTFFEIYNGKLFDLLNKKAKLRVLEDGKQQVQVVGLQEHLVNSADDVIKMIDMGSACR---------NSSRSHACFQIILRAKGRMHGKFSLVDLAGNE---------------GAEINKSLLALKECIRALGQNKAHTPFRESKLTQVLRDSFIGENSRTCMIATISPGISSCEYTLNTLRYADRVKE 587
                                   238       248       258       268       278       288       298       308       318       328       338       348       358|        -  |    378       388       398       408       418       428       438       448       | -       468       478       488        |-         -    |  518       528       538       548       558       568       578         
                                                                                                                                                            359         371                                                                                  456       466                            497             513                                                                          

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HEH)

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KIF2C_HUMAN | Q99661)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0019237    centromeric DNA binding    Interacting selectively and non-covalently with a centromere, a region of chromosome where the spindle fibers attach during mitosis and meiosis.
    GO:0008017    microtubule binding    Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
    GO:0003777    microtubule motor activity    Catalysis of movement along a microtubule, coupled to the hydrolysis of a nucleoside triphosphate (usually ATP).
    GO:0051010    microtubule plus-end binding    Interacting selectively and non-covalently with the plus end of a microtubule.
    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).
biological process
    GO:0019886    antigen processing and presentation of exogenous peptide antigen via MHC class II    The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein.
    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:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0007059    chromosome segregation    The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
    GO:0030951    establishment or maintenance of microtubule cytoskeleton polarity    Any cellular process that results in the specification, formation or maintenance of polarized microtubule-based cytoskeletal structures.
    GO:0007019    microtubule depolymerization    The removal of tubulin heterodimers from one or both ends of a microtubule.
    GO:0007018    microtubule-based movement    A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules.
    GO:0007080    mitotic metaphase plate congression    The cell cycle process in which chromosomes are aligned at the metaphase plate, a plane halfway between the poles of the mitotic spindle, during mitosis.
    GO:0051983    regulation of chromosome segregation    Any process that modulates the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets.
    GO:0006890    retrograde vesicle-mediated transport, Golgi to ER    The directed movement of substances from the Golgi back to the endoplasmic reticulum, mediated by vesicles bearing specific protein coats such as COPI or COG.
    GO:0007062    sister chromatid cohesion    The cell cycle process in which the sister chromatids of a replicated chromosome become tethered to each other.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000775    chromosome, centromeric region    The region of a chromosome that includes the centromeric DNA and associated proteins. 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:0000777    condensed chromosome kinetochore    A multisubunit complex that is located at the centromeric region of a condensed chromosome and provides an attachment point for the spindle microtubules.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005881    cytoplasmic microtubule    Any microtubule in the cytoplasm of a cell.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    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:0005871    kinesin complex    Any complex that includes a dimer of molecules from the kinesin superfamily, a group of related proteins that contain an extended region of predicted alpha-helical coiled coil in the main chain that likely produces dimerization. The native complexes of several kinesin family members have also been shown to contain additional peptides, often designated light chains as all of the noncatalytic subunits that are currently known are smaller than the chain that contains the motor unit. Kinesin complexes generally possess a force-generating enzymatic activity, or motor, which converts the free energy of the gamma phosphate bond of ATP into mechanical work.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    GO:0015630    microtubule cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.
    GO:0035371    microtubule plus-end    The growing (plus) end of a microtubule. In vitro, microtubules polymerize more quickly at the plus end than at the minus end. In vivo, microtubule growth occurs only at the plus end, and the plus end switches between periods of growth and shortening, a behavior known as dynamic instability.
    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.

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 Related Entries

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

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        KIF2C_HUMAN | Q996614ubf 4y05

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