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(-) Description

Title :  SOLUTION STRUCTURE OF THE FIRST AND SECOND PHD DOMAIN FROM MYELOID/LYMPHOID OR MIXED-LINEAGE LEUKEMIA PROTEIN 3 HOMOLOG
 
Authors :  X. R. Qin, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  03 Apr 07  (Deposition) - 09 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Phd Domain, Myeloid/Lymphoid Or Mixed-Lineage Leukemia Protein, Histone-Lysine N-Methyltransferase, H3 Lysine-4 Specific Mll3, Homologous To Alr Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. R. Qin, F. Hayashi, S. Yokoyama
Solution Structure Of The First And Second Phd Domain From Myeloid/Lymphoid Or Mixed-Lineage Leukemia Protein 3 Homolog
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MYELOID/LYMPHOID OR MIXED-LINEAGE LEUKEMIA PROTEIN 3 HOMOLOG
    ChainsA
    EC Number2.1.1.43
    EngineeredYES
    Expression System PlasmidP070115-52
    Expression System Vector TypePLASMID
    FragmentPHD DOMAIN
    GeneMLL3, HALR, KIAA1506
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymHISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-4 SPECIFIC MLL3, HOMOLOGOUS TO ALR PROTEIN

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

NMR Structure (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION

(-) Sites  (4, 4)

NMR Structure (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:10 , CYS A:13 , HIS A:33 , CYS A:36BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWARECYS A:25 , CYS A:28 , CYS A:51 , CYS A:54BINDING SITE FOR RESIDUE ZN A 501
3AC3SOFTWARECYS A:57 , CYS A:60 , HIS A:80 , CYS A:83BINDING SITE FOR RESIDUE ZN A 701
4AC4SOFTWARECYS A:72 , CYS A:75 , CYS A:98 , CYS A:101BINDING SITE FOR RESIDUE ZN A 901

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 20)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Gln A:85 -Pro A:86

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

NMR Structure (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_036311C347GKMT2C_HUMANUnclassified  ---AC13G
2CancerSNPVAR_KMT2C_HUMAN_CCDS5931_1_01 *C347GKMT2C_HUMANDisease (Colorectal cancer)  ---AC13G
3UniProtVAR_036312D400NKMT2C_HUMANUnclassified  ---AD66N
4CancerSNPVAR_KMT2C_HUMAN_CCDS5931_1_02 *D400NKMT2C_HUMANDisease (Colorectal cancer)  ---AD66N
   * ID not provided by source

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

(-) PROSITE Motifs  (4, 7)

NMR Structure (4, 7)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_PHD_2PS50016 Zinc finger PHD-type profile.KMT2C_HUMAN341-391
388-438
464-520
957-1010
1007-1057
1084-1139
  2A:8-57
A:54-104
-
-
-
-
2ZF_PHD_1PS01359 Zinc finger PHD-type signature.KMT2C_HUMAN344-409
359-459
435-517
960-1028
977-1054
  3A:10-75
A:25-110
A:101-110
-
-
3ZF_RING_2PS50089 Zinc finger RING-type profile.KMT2C_HUMAN344-389  1A:10-55
4DHHCPS50216 DHHC domain profile.KMT2C_HUMAN436-473  1A:102-110

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003551932aENSE00001642231chr7:152133090-152132711380KMT2C_HUMAN1-54540--
1.3ENST000003551933ENSE00001779646chr7:152055760-15205567289KMT2C_HUMAN54-84310--
1.5cENST000003551935cENSE00001596960chr7:152027824-152027686139KMT2C_HUMAN84-130470--
1.6bENST000003551936bENSE00001774010chr7:152012423-152012223201KMT2C_HUMAN130-197680--
1.7bENST000003551937bENSE00001749065chr7:152009031-152008883149KMT2C_HUMAN197-247511A:1-44
1.8aENST000003551938aENSE00001803163chr7:152007160-152007051110KMT2C_HUMAN247-283371A:4-7 (gaps)34
1.9ENST000003551939ENSE00001783379chr7:151970952-151970790163KMT2C_HUMAN284-338550--
1.10ENST0000035519310ENSE00001799851chr7:151962294-151962123172KMT2C_HUMAN338-395581A:8-6154
1.11ENST0000035519311ENSE00001721204chr7:151960215-151960101115KMT2C_HUMAN395-433391A:61-9939
1.12ENST0000035519312ENSE00001629216chr7:151949800-151949631170KMT2C_HUMAN434-490571A:100-111 (gaps)13
1.13ENST0000035519313ENSE00001666640chr7:151949175-151949024152KMT2C_HUMAN490-541520--
1.14ENST0000035519314ENSE00001791110chr7:151948051-151947938114KMT2C_HUMAN541-579390--
1.15ENST0000035519315ENSE00001635330chr7:151947038-15194696178KMT2C_HUMAN579-605270--
1.16aENST0000035519316aENSE00001712229chr7:151945705-151944987719KMT2C_HUMAN605-8442400--
1.17bENST0000035519317bENSE00001613372chr7:151935911-151935792120KMT2C_HUMAN845-884400--
1.19ENST0000035519319ENSE00001619203chr7:151933018-151932902117KMT2C_HUMAN885-923390--
1.20ENST0000035519320ENSE00001758947chr7:151927406-151927305102KMT2C_HUMAN924-957340--
1.21bENST0000035519321bENSE00001726293chr7:151927112-151927008105KMT2C_HUMAN958-992350--
1.22ENST0000035519322ENSE00000730374chr7:151921701-151921520182KMT2C_HUMAN993-1053610--
1.23bENST0000035519323bENSE00001630291chr7:151921264-151921100165KMT2C_HUMAN1053-1108560--
1.25ENST0000035519325ENSE00001754170chr7:151919767-151919658110KMT2C_HUMAN1108-1145380--
1.26cENST0000035519326cENSE00000730386chr7:151919151-15191908666KMT2C_HUMAN1145-1167230--
1.27aENST0000035519327aENSE00001628944chr7:151917820-151917608213KMT2C_HUMAN1167-1238720--
1.28ENST0000035519328ENSE00000730393chr7:151904513-151904385129KMT2C_HUMAN1238-1281440--
1.29ENST0000035519329ENSE00000730396chr7:151902310-151902191120KMT2C_HUMAN1281-1321410--
1.30ENST0000035519330ENSE00000430342chr7:151900149-151900019131KMT2C_HUMAN1321-1364440--
1.31ENST0000035519331ENSE00000730402chr7:151896544-151896364181KMT2C_HUMAN1365-1425610--
1.32ENST0000035519332ENSE00000730404chr7:151893096-151892992105KMT2C_HUMAN1425-1460360--
1.33ENST0000035519333ENSE00000730409chr7:151891653-151891525129KMT2C_HUMAN1460-1503440--
1.34ENST0000035519334ENSE00000730414chr7:151891346-15189131433KMT2C_HUMAN1503-1514120--
1.35ENST0000035519335ENSE00000730416chr7:151891213-151891094120KMT2C_HUMAN1514-1554410--
1.36ENST0000035519336ENSE00000430344chr7:151884932-151884800133KMT2C_HUMAN1554-1598450--
1.37ENST0000035519337ENSE00000730421chr7:151884561-151884347215KMT2C_HUMAN1598-1670730--
1.38ENST0000035519338ENSE00000730423chr7:151882716-15188264374KMT2C_HUMAN1670-1694250--
1.39ENST0000035519339ENSE00000730426chr7:151880241-151880059183KMT2C_HUMAN1695-1755610--
1.40ENST0000035519340ENSE00000730429chr7:151879679-1518777961884KMT2C_HUMAN1756-23836280--
1.41ENST0000035519341ENSE00000730434chr7:151877211-151876919293KMT2C_HUMAN2384-2481980--
1.42aENST0000035519342aENSE00000730439chr7:151875095-1518732761820KMT2C_HUMAN2481-30886080--
1.43ENST0000035519343ENSE00000730441chr7:151871327-151871216112KMT2C_HUMAN3088-3125380--
1.44ENST0000035519344ENSE00000730442chr7:151868427-15186834979KMT2C_HUMAN3125-3151270--
1.45ENST0000035519345ENSE00000430311chr7:151866334-15186627164KMT2C_HUMAN3152-3173220--
1.46ENST0000035519346ENSE00000730443chr7:151864463-151864231233KMT2C_HUMAN3173-3250780--
1.47aENST0000035519347aENSE00000730444chr7:151860911-1518592021710KMT2C_HUMAN3251-38205700--
1.48bENST0000035519348bENSE00000730447chr7:151856157-151855942216KMT2C_HUMAN3821-3892720--
1.49ENST0000035519349ENSE00000730450chr7:151855010-151854846165KMT2C_HUMAN3893-3947550--
1.50aENST0000035519350aENSE00000730453chr7:151853431-151853290142KMT2C_HUMAN3948-3995480--
1.51ENST0000035519351ENSE00000730457chr7:151853142-151852995148KMT2C_HUMAN3995-4044500--
1.53ENST0000035519353ENSE00000730460chr7:151851530-151851352179KMT2C_HUMAN4044-4104610--
1.54ENST0000035519354ENSE00000730462chr7:151851231-151851095137KMT2C_HUMAN4104-4149460--
1.55cENST0000035519355cENSE00000430326chr7:151850039-151849790250KMT2C_HUMAN4150-4233840--
1.56ENST0000035519356ENSE00000730467chr7:151848666-151848527140KMT2C_HUMAN4233-4279470--
1.57ENST0000035519357ENSE00000730470chr7:151848092-151847985108KMT2C_HUMAN4280-4315360--
1.58ENST0000035519358ENSE00000730472chr7:151846237-1518451181120KMT2C_HUMAN4316-46893740--
1.59ENST0000035519359ENSE00000730474chr7:151843820-151843684137KMT2C_HUMAN4689-4734460--
1.60bENST0000035519360bENSE00000730475chr7:151842380-151842238143KMT2C_HUMAN4735-4782480--
1.61ENST0000035519361ENSE00000730477chr7:151841966-151841798169KMT2C_HUMAN4782-4838570--
1.63bENST0000035519363bENSE00000730479chr7:151836876-151836760117KMT2C_HUMAN4839-4877390--
1.64ENST0000035519364ENSE00000730480chr7:151836344-15183627174KMT2C_HUMAN4878-4902250--
1.65aENST0000035519365aENSE00000730481chr7:151835989-151835881109KMT2C_HUMAN4902-4938370--
1.65eENST0000035519365eENSE00001424024chr7:151834009-1518320141996KMT2C_HUMAN4939-4968300--

(-) 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:111
 aligned with KMT2C_HUMAN | Q8NEZ4 from UniProtKB/Swiss-Prot  Length:4911

    Alignment length:203
                                   253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443   
          KMT2C_HUMAN   244 DSTGTCWAHHRCVEWSLGVCQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQDFSHIFLLCPEHIDQAPERSKEDANCAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAVTPLKRAGWQCPECKVCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNCRICIECGTRSS 446
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....------------------------------..-------------------------------------------------------------...............ee......ee....................................eee......eee.hhh.............hhhhhh...-..... Sec.struct. author
             SAPs(SNPs) (1) -------------------------------------------------------------------------------------------------------G----------------------------------------------------N---------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------------------------------------------------------G----------------------------------------------------N---------------------------------------------- SAPs(SNPs) (2)
                PROSITE (1) -------------------------------------------------------------------------------------------------ZF_PHD_2  PDB: A:8-57 UniProt: 341-391             -------------------------------------------ZF_PHD_1     PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------ZF_PHD_2  PDB: A:54-104 UniProt: 388-438        DHHC        PROSITE (2)
                PROSITE (3) ----------------------------------------------------------------------------------------------------ZF_RING_2  PDB: A:10-55 UniProt: 344-389      --------------------------------------------------------- PROSITE (3)
                PROSITE (4) ----------------------------------------------------------------------------------------------------ZF_PHD_1  PDB: A:10-75 UniProt: 344-409                           ------------------------------------- PROSITE (4)
                PROSITE (5) -------------------------------------------------------------------------------------------------------------------ZF_PHD_1  PDB: A:25-110 UniProt: 359-459                                                 PROSITE (5)
           Transcript 1 (1) 1.7b------------------------------------------------------------------------------------------Exon 1.10  PDB: A:8-61 UniProt: 338-395 [INCOMPLETE]      --------------------------------------Exon 1.12     Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.8a  PDB: A:4-7 (gaps)         Exon 1.9  PDB: - UniProt: 284-338                      --------------------------------------------------------Exon 1.11  PDB: A:61-99                ------------- Transcript 1 (2)
                 2ysm A   1 GSSGS------------------------------SG-------------------------------------------------------------ANCAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAVTPLKRAGWQCPECKVCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNCRICIS-GPSSG 111
                                |    -         -         -     ||  -         -         -         -         -         -        |9        19        29        39        49        59        69        79        89        99      |108   
                                5                              6|                                                             8                                                                                               106 |    
                                                                7                                                                                                                                                               107    

   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 2YSM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

NMR Structure(hide GO term definitions)
Chain A   (KMT2C_HUMAN | Q8NEZ4)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0042800    histone methyltransferase activity (H3-K4 specific)    Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 4) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 4). This reaction is the addition of a methyl group onto lysine at position 4 of the histone H3 protein.
    GO:0018024    histone-lysine N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine. The methylation of peptidyl-lysine in histones forms N6-methyl-L-lysine, N6,N6-dimethyl-L-lysine and N6,N6,N6-trimethyl-L-lysine derivatives.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0051568    histone H3-K4 methylation    The modification of histone H3 by addition of one or more methyl groups to lysine at position 4 of the histone.
    GO:0034968    histone lysine methylation    The modification of a histone by addition of one or more methyl groups to a lysine residue.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0044666    MLL3/4 complex    A protein complex that can methylate lysine-4 of histone H3, and which contains either of the protein subunits MLL3 or MLL4 in mammals, or equivalent in other species.
    GO:0035097    histone methyltransferase complex    A multimeric complex that is able to catalyze the addition of methyl groups to histone proteins.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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)

UniProtKB/Swiss-Prot
        KMT2C_HUMAN | Q8NEZ42yuk 3uvl 4ery 5f59 5f6k

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2YSM)