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(-) Description

Title :  CRYSTAL STRUCTURE OF DNMT3A ADD DOMAIN G550D MUTANT BOUND TO H3 PEPTIDE
 
Authors :  H. Wang, H. Li
Date :  08 May 14  (Deposition) - 13 May 15  (Release) - 13 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,C,E,P
Biol. Unit 1:  A,P  (1x)
Biol. Unit 2:  C,E  (1x)
Keywords :  Zinc Finger, Histone Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Noh, H. Wang, H. Kim, W. Wenderski, F. Fang, C. Li, S. Dewell, X. Wu, A. Ferris, S. H. Hughes, D. Zheng, A. M. Melnick, D. J. Patel, H. Li, C. D. Allis
Engineering Of A Histone-Recognition Domain In A De Novo Dn Methyltransferase Alters The Epigenetic Landscape Of Escs
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DNA (CYTOSINE-5)-METHYLTRANSFERASE 3A
    Chains: A, C
    EC Number: 2.1.1.37
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: ADD DOMAIN, UNP RESIDUES 476-611
    Gene: DNMT3A
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DNMT3A, DNA METHYLTRANSFERASE HSAIIIA, DNA MTASE HSAIIIA, M.HSAIIIA
 
Molecule 2 - HISTONE H3
    Chains: P, E
    Engineered: YES
    Fragment: H3 N-TERMINAL
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ACEP
Biological Unit 1 (1x): A  P
Biological Unit 2 (1x):  CE 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1ZN6Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:549 , CYS A:554 , CYS A:583 , CYS A:586BINDING SITE FOR RESIDUE ZN A 701
2AC2SOFTWARECYS A:537 , CYS A:540 , CYS A:559 , CYS A:562BINDING SITE FOR RESIDUE ZN A 702
3AC3SOFTWARECYS A:494 , CYS A:497 , CYS A:514 , CYS A:517BINDING SITE FOR RESIDUE ZN A 703
4AC4SOFTWARECYS C:549 , CYS C:554 , CYS C:583 , CYS C:586BINDING SITE FOR RESIDUE ZN C 701
5AC5SOFTWARECYS C:537 , CYS C:540 , CYS C:559 , CYS C:562BINDING SITE FOR RESIDUE ZN C 702
6AC6SOFTWARECYS C:494 , CYS C:497 , CYS C:514 , CYS C:517BINDING SITE FOR RESIDUE ZN C 703

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp A:579 -Pro A:580
2Asp C:579 -Pro C:580

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QBR)

(-) 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:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh...hhhhh..........ee......eehhhhhhhhhhhh...................eeee........eeehhhhhhhh..hhhhhhhhh............ee..ee...hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qbr A 475 SRERLVYEVRQKCRNIEDICISCGSLNVTLEHPLFVGGMCQNCKNCFLECAYQYDDDGYQSYCTICCGGREVLMCDNNNCCRCFCVECVDLLVGPGAAQAAIKEDPWNCYMCGHKGTYGLLRRREDWPSRLQMFFA 610
                                   484       494       504       514       524       534       544       554       564       574       584       594       604      


Chain C from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh...hhhhh..........ee......eehhhhhhhhhhhh...................eeee........eeehhhhhhhh..hhhhhhhhh............ee..ee...hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qbr C 475 SRERLVYEVRQKCRNIEDICISCGSLNVTLEHPLFVGGMCQNCKNCFLECAYQYDDDGYQSYCTICCGGREVLMCDNNNCCRCFCVECVDLLVGPGAAQAAIKEDPWNCYMCGHKGTYGLLRRREDWPSRLQMFFA 610
                                   484       494       504       514       524       534       544       554       564       574       584       594       604      


Chain E from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author .eeee.. Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 4qbr E   1 ARTKQTA   7


Chain P from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author .eeee.. Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 4qbr P   1 ARTKQTA   7
   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 4QBR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (77, 82)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        DNM3A_HUMAN | Q9Y6K1: 2qrv 3a1a 3a1b 3llr 3svm 4qbq 4qbs 4u7p 4u7t
        H31_HUMAN | P68431: 1cs9 1ct6 1guw 1o9s 1q3l 2b2t 2b2u 2b2v 2b2w 2c1j 2c1n 2cv5 2kwj 2kwk 2l75 2lbm 2m0o 2ndf 2ndg 2oq6 2ot7 2ox0 2ri7 2uxn 2v89 2vpg 2x0l 3a1b 3afa 3avr 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3b95 3kmt 3kqi 3lqi 3lqj 3o34 3o35 3o37 3qj6 3rig 3riy 3sou 3sow 3u31 3u3d 3u4s 3u5n 3u5o 3u5p 3uee 3uef 3uig 3uii 3uik 3v43 3w96 3w97 3w98 3w99 3wa9 3waa 3wkj 3x1s 3x1t 3x1u 3x1v 3zg6 3zvy 4a0j 4a0n 4a7j 4bd3 4c1q 4f4u 4f56 4ft2 4ft4 4fwf 4hon 4i51 4l7x 4lk9 4lka 4llb 4lxl 4n4h 4qbq 4qbs 4tn7 4u68 4up0 4uy4 4x3k 4y6l 4yhp 4yhz 4ym5 4ym6 4z0r 4z2m 5av5 5av6 5av8 5av9 5avb 5avc 5b24 5b2i 5b2j 5b31 5c11 5c13 5c3i 5cpi 5cpj 5cpk 5d6y 5dah 5fb0 5fb1 5ffv 5gse 5gsu 5gt0 5gt3 5gtc 5hjb 5hjc 5hjd 5hyn 5iql 5j3v 5j9s 5jhn 5jin 5jiy 5jj0 5jrg 5kjh 5kji 5kkl 5m5g 5svx 5svy 5t0k 5t0m 5t1g 5t1i 5t8r 5tbn 5tdr 5tdw 5v21 5v22 5va6

(-) Related Entries Specified in the PDB File

4qbq 4qbs