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(-) Description

Title :  STRUCTURES AND CHEMICAL SHIFT ASSIGNMENTS FOR THE ADD DOMAIN OF THE ATRX PROTEIN
 
Authors :  J. Yang, D. Neuhaus
Date :  13 Sep 06  (Deposition) - 26 Jun 07  (Release) - 23 Jun 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (32x)
Keywords :  Add Domain, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Argentaro, J. C. Yang, L. Chapman, M. S. Kowalczyk, R. J. Gibbons, D. R. Higgs, D. Neuhaus, D. Rhodes
Structural Consequences Of Disease-Causing Mutations In The Atrx-Dnmt3-Dnmt3L (Add) Domain Of The Chromatin-Associated Protein Atrx.
Proc. Natl. Acad. Sci. Usa V. 104 11939 2007
PubMed-ID: 17609377  |  Reference-DOI: 10.1073/PNAS.0704057104

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR ATRX
    ChainsA
    EC Number3.6.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET30A
    Expression System StrainBL21 DE3 ROSETTA PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentADD DOMAIN, RESIDUES 159-296
    GeneATRX, RAD54L, XH2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymATP-DEPENDENT HELICASE ATRX, X-LINKED HELICASE II, X-LINKED NUCLEAR PROTEIN, XNP, ZNF- HX

 Structural Features

(-) Chains, Units

  
NMR Structure (32x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

NMR Structure (1, 3)
No.NameCountTypeFull Name
1ZN3Ligand/IonZINC ION

(-) Sites  (3, 3)

NMR Structure (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:171 , CYS A:174 , CYS A:197 , CYS A:200BINDING SITE FOR RESIDUE ZN A 1
2AC2SOFTWARECYS A:220 , CYS A:223 , CYS A:240 , CYS A:243BINDING SITE FOR RESIDUE ZN A 2
3AC3SOFTWARECYS A:232 , CYS A:235 , CYS A:265 , CYS A:268BINDING SITE FOR RESIDUE ZN A 3

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JM1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2JM1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (17, 17)

NMR Structure (17, 17)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_012113G175EATRX_HUMANDisease (ATRX)  ---AG175E
02UniProtVAR_012115N179SATRX_HUMANDisease (ATRX)  ---AN179S
03UniProtVAR_001226P190AATRX_HUMANDisease (ATRX)  ---AP190A
04UniProtVAR_012116P190LATRX_HUMANDisease (ATRX)  ---AP190L
05UniProtVAR_012117P190SATRX_HUMANDisease (ATRX)  ---AP190S
06UniProtVAR_001227L192FATRX_HUMANDisease (ATRX)  ---AL192F
07UniProtVAR_012118V194IATRX_HUMANDisease (ATRX)  ---AV194I
08UniProtVAR_001228C200SATRX_HUMANDisease (ATRX)  ---AC200S
09UniProtVAR_012119Q219PATRX_HUMANDisease (ATRX)  ---AQ219P
10UniProtVAR_001229C220RATRX_HUMANDisease (ATRX)  ---AC220R
11UniProtVAR_032625C220YATRX_HUMANDisease (MRXSHF1)  ---AC220Y
12UniProtVAR_001230W222SATRX_HUMANDisease (ATRX)  ---AW222S
13UniProtVAR_001231C243FATRX_HUMANDisease (ATRX)  ---AC243F
14UniProtVAR_001232R246CATRX_HUMANDisease (ATRX)  ---AR246C
15UniProtVAR_010914R246LATRX_HUMANDisease (ATRX)  ---AR246L
16UniProtVAR_012120G249CATRX_HUMANDisease (ATRX)  ---AG249C
17UniProtVAR_001233G249DATRX_HUMANDisease (ATRX)  ---AG249D

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADDPS51533 ADD domain profile.ATRX_HUMAN159-296  1A:160-296

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003733441aENSE00002167359X:77041702-77041468235ATRX_HUMAN1-770--
1.2ENST000003733442ENSE00001636919X:76972720-76972608113ATRX_HUMAN7-45390--
1.4bENST000003733444bENSE00001688675X:76954117-7695406256ATRX_HUMAN45-63190--
1.5ENST000003733445ENSE00001763951X:76953123-7695307153ATRX_HUMAN64-81180--
1.6ENST000003733446ENSE00001652735X:76952192-76952065128ATRX_HUMAN81-124440--
1.7aENST000003733447aENSE00002168990X:76949426-76949313114ATRX_HUMAN124-162391A:156-162 (gaps)13
1.9ENST000003733449ENSE00002165776X:76944420-76944311110ATRX_HUMAN162-198371A:162-19837
1.10ENST0000037334410ENSE00001694382X:76940498-7694043168ATRX_HUMAN199-221231A:199-22123
1.11bENST0000037334411bENSE00002071055X:76940085-769370123074ATRX_HUMAN221-124610261A:221-29676
1.12aENST0000037334412aENSE00001638399X:76931793-7693172173ATRX_HUMAN1246-1270250--
1.13ENST0000037334413ENSE00001655114X:76920267-76920134134ATRX_HUMAN1270-1315460--
1.14ENST0000037334414ENSE00001618412X:76919047-76918871177ATRX_HUMAN1315-1374600--
1.15ENST0000037334415ENSE00001759922X:76912143-7691205094ATRX_HUMAN1374-1405320--
1.16ENST0000037334416ENSE00002155398X:76909690-76909588103ATRX_HUMAN1405-1439350--
1.17ENST0000037334417ENSE00001804555X:76907843-76907604240ATRX_HUMAN1440-1519800--
1.18ENST0000037334418ENSE00001692523X:76891547-76891406142ATRX_HUMAN1520-1567480--
1.19aENST0000037334419aENSE00001634558X:76890194-76890085110ATRX_HUMAN1567-1603370--
1.20aENST0000037334420aENSE00001729307X:76889200-76889054147ATRX_HUMAN1604-1652490--
1.21ENST0000037334421ENSE00001679104X:76888872-76888695178ATRX_HUMAN1653-1712600--
1.22ENST0000037334422ENSE00001611054X:76876000-76875863138ATRX_HUMAN1712-1758470--
1.23ENST0000037334423ENSE00001600235X:76874449-76874274176ATRX_HUMAN1758-1816590--
1.24ENST0000037334424ENSE00001614801X:76872198-76872081118ATRX_HUMAN1817-1856400--
1.26bENST0000037334426bENSE00001611019X:76856033-76855903131ATRX_HUMAN1856-1899440--
1.27bENST0000037334427bENSE00001762228X:76855289-7685520189ATRX_HUMAN1900-1929300--
1.28ENST0000037334428ENSE00001627804X:76855049-76854880170ATRX_HUMAN1929-1986580--
1.29ENST0000037334429ENSE00001690714X:76849319-76849166154ATRX_HUMAN1986-2037520--
1.30ENST0000037334430ENSE00001637691X:76845410-76845304107ATRX_HUMAN2037-2073370--
1.31ENST0000037334431ENSE00001632927X:76829823-76829715109ATRX_HUMAN2073-2109370--
1.32ENST0000037334432ENSE00001674842X:76814317-76814140178ATRX_HUMAN2109-2168600--
1.33ENST0000037334433ENSE00001762255X:76813116-76812922195ATRX_HUMAN2169-2233650--
1.34ENST0000037334434ENSE00001605899X:76778879-76778730150ATRX_HUMAN2234-2283500--
1.35ENST0000037334435ENSE00001640278X:76777866-76777741126ATRX_HUMAN2284-2325420--
1.36ENST0000037334436ENSE00001609746X:76776976-7677688196ATRX_HUMAN2326-2357320--
1.37ENST0000037334437ENSE00001620267X:76776394-76776266129ATRX_HUMAN2358-2400430--
1.38ENST0000037334438ENSE00001885562X:76764107-767603783730ATRX_HUMAN2401-2492920--

(-) Sequences/Alignments

NMR Structure
   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:141
 aligned with ATRX_HUMAN | P46100 from UniProtKB/Swiss-Prot  Length:2492

    Alignment length:147
                                   159       169       179       189       199       209       219       229       239       249       259       269       279       289       
           ATRX_HUMAN   150 SKMKTENLKKRGEDGLHGIVSCTACGQQVNHFQKDSIYRHPSLQVLICKNCFKYYMSDDISRDSDGMDEQCRWCAEGGNLICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHPEPLLDLVTACNSVFENLEQLLQQNKK 296
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....------...........................ee......eehhhhhhhhhhh.....................eee......eeehhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
             SAPs(SNPs) (1) -------------------------E---S----------A-F-I-----S------------------PR-S--------------------F--C--C----------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------L-----------------------------Y-------------------------L--D----------------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ----------------------------------------S---------------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
                    PROSITE ---------ADD  PDB: A:160-296 UniProt: 159-296                                                                                                       PROSITE
           Transcript 1 (1) Exon 1.7a    ------------------------------------Exon 1.10              --------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.9  PDB: A:162-198             ----------------------Exon 1.11b  PDB: A:221-296 UniProt: 221-1246 [INCOMPLETE]                    Transcript 1 (2)
                 2jm1 A 156 GAMK------RGEDGLHGIVSCTACGQQVNHFQKDSIYRHPSLQVLICKNCFKYYMSDDISRDSDGMDEQCRWCAEGGNLICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHPEPLLDLVTACNSVFENLEQLLQQNKK 296
                               |     -|      169       179       189       199       209       219       229       239       249       259       269       279       289       
                             159    160                                                                                                                                        

   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 2JM1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2JM1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2JM1)

(-) Gene Ontology  (51, 51)

NMR Structure(hide GO term definitions)
Chain A   (ATRX_HUMAN | P46100)
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:0003678    DNA helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA helix.
    GO:0015616    DNA translocase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive movement along a single- or double-stranded DNA molecule.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0070087    chromo shadow domain binding    Interacting selectively and non-covalently with a chromo shadow domain, a protein domain that is distantly related, and found in association with, the chromo domain.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0035064    methylated histone binding    Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
    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:0030330    DNA damage response, signal transduction by p53 class mediator    A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage.
    GO:0032508    DNA duplex unwinding    The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.
    GO:0006306    DNA methylation    The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006336    DNA replication-independent nucleosome assembly    The formation of nucleosomes outside the context of DNA replication.
    GO:0060009    Sertoli cell development    The process whose specific outcome is the progression of a Sertoli cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a Sertoli cell fate.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0072711    cellular response to hydroxyurea    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydroxyurea stimulus.
    GO:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    GO:0030900    forebrain development    The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions).
    GO:0035264    multicellular organism growth    The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
    GO:1904908    negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric    Any process that stops, prevents or reduces the frequency, rate or extent of maintenance of mitotic sister chromatid cohesion, telomeric.
    GO:1901581    negative regulation of telomeric RNA transcription from RNA pol II promoter    Any process that stops, prevents or reduces the frequency, rate or extent of telomeric RNA transcription from RNA pol II promoter.
    GO:0006334    nucleosome assembly    The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
    GO:0010571    positive regulation of nuclear cell cycle DNA replication    Any process that activates or increases the frequency, rate or extent of The DNA-dependent DNA replication that occurs in the nucleus of eukaryotic organisms as part of the cell cycle.
    GO:0032206    positive regulation of telomere maintenance    Any process that activates or increases the frequency, rate or extent of a process that affects and monitors the activity of telomeric proteins and the length of telomeric DNA.
    GO:1901582    positive regulation of telomeric RNA transcription from RNA pol II promoter    Any process that activates or increases the frequency, rate or extent of telomeric RNA transcription from RNA pol II promoter.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0035128    post-embryonic forelimb morphogenesis    The process, occurring after embryonic development, by which the anatomical structures of the forelimb are generated and organized. The forelimbs are the front limbs of an organism.
    GO:0070198    protein localization to chromosome, telomeric region    Any process in which a protein is transported to, or maintained at, the telomeric region of a chromosome.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0031297    replication fork processing    The process in which a DNA replication fork that has stalled is restored to a functional state and replication is restarted. The stalling may be due to DNA damage, DNA secondary structure, bound proteins, dNTP shortage, or other causes.
    GO:0072520    seminiferous tubule development    The reproductive developmental process whose specific outcome is the progression of the seminiferous tubule over time, from its formation to the mature structure. Seminiferous tubules are ducts located in the testicles, and are the specific location of meiosis, and the subsequent creation of gametes, namely spermatozoa.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0016605    PML body    A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection.
    GO:0070603    SWI/SNF superfamily-type complex    A protein complex that contains an ortholog of the Saccharomyces ATPase Swi2/Snf2 as one of the core components and mediates assembly of nucleosomes, changes to the spacing or structure of nucleosomes, or some combination of those activities in a manner that requires ATP.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000781    chromosome, telomeric region    The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0000792    heterochromatin    A compact and highly condensed form of chromatin.
    GO:0000228    nuclear chromosome    A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0005720    nuclear heterochromatin    A condensed form of chromatin, occurring in the nucleus during interphase, that stains strongly with basophilic dyes. The DNA of heterochromatin is typically replicated at a later stage in the cell-division cycle than euchromatin.
    GO:1990707    nuclear subtelomeric heterochromatin    Heterochromatic regions of the chromosome found at the subtelomeric regions of a chromosome in the nucleus.
    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.
    GO:0005721    pericentric heterochromatin    Heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by the modified histone H3K9me3.
    GO:0031933    telomeric heterochromatin    Heterochromatic regions of the chromosome found at the telomeres.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ATRX_HUMAN | P461002lbm 2ld1 3ql9 3qla 3qlc 3qln 4w5a

(-) Related Entries Specified in the PDB File

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