3QKJ: PDB entry 3QKJ

Name: PDB 3QKJ: The PWWP domain of human DNA (CYTOSINE-5-)-METHYLTRANSFERASE 3 BETA in complex with a bis-tris molecule
Published: 2011-03-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

The PWWP domain of human DNA (CYTOSINE-5-)-METHYLTRANSFERASE 3 BETA in complex with a bis-tris molecule. Determined by X-ray diffraction at 2.04 Å resolution. Released 9 Mar 2011.

Method: X-ray diffraction
Resolution: 2.04 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,474
Mol. weight: 68.44 kDa
Ligands: BTB
Released: 9 Mar 2011

Explore 3QKJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3QKJ contains 30 α-helices and 20 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	228-231	4	1
β-strand	239-244	6	1
α-helix	246-248	3
α-helix	253-255	3
β-strand	258-263	6	1
β-strand	269-273	5	1
α-helix	274-276	3
β-strand	277-279	3	1
α-helix	289-294	6
α-helix	296-313	18
α-helix	329-337	9
α-helix	344-348	5

Chain B: 8 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	228-231	4	2
β-strand	239-244	6	2
α-helix	246-248	3
α-helix	253-255	3
β-strand	258-263	6	2
β-strand	269-273	5	2
α-helix	274-276	3
β-strand	277-279	3	2
α-helix	283-286	4
α-helix	289-294	6
α-helix	296-313	18
α-helix	326-337	12
α-helix	344-348	5

Chain C: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	228-231	4	3
β-strand	239-244	6	3
α-helix	246-248	3
α-helix	253-255	3
β-strand	258-263	6	3
β-strand	269-273	5	3
β-strand	277-279	3	3
α-helix	283-286	4
α-helix	289-294	6
α-helix	296-313	18
α-helix	325-337	13
α-helix	344-348	5

Chain D: 8 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	228-231	4	4
β-strand	239-244	6	4
α-helix	246-248	3
α-helix	253-255	3
β-strand	258-263	6	4
β-strand	269-273	5	4
α-helix	274-276	3
β-strand	277-279	3	4
α-helix	283-286	4
α-helix	289-294	6
α-helix	296-313	18
α-helix	325-337	13
α-helix	344-348	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA cytosine-5 methyltransferase 3 beta isoform 6 variant	A, B, C, D	protein	151	Homo sapiens	Q9UBC3 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>3QKJ_1 DNA cytosine-5 methyltransferase 3 beta isoform 6 variant (chains A, B, C, D)
GEADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWF
GDGKFSEVSADKLVALGLFSQHFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDS
LEDQLKPMLEWAHGGFKPTGIEGLKPNNTQP

Ligands and cofactors

ID	Name	Formula	Copies
BTB	2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol	C8 H19 N O5	4

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structural and Histone Binding Ability Characterizations of Human PWWP Domains. Wu, H., Zeng, H., Lam, R. et al. PLoS One (2011) 6:e18919-e18919. DOI 10.1371/journal.pone.0018919 · PubMed

Other PDB entries of the same protein (UniProt Q9UBC3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NRR 1.7 Å, Human DNMT3B PWWP domain in complex with 5-[(2-Hydroxyethyl)(propyl)amino]-1-pentanol
3FLG 1.8 Å, The PWWP domain of Human DNA (cytosine-5-)-methyltransferase 3 beta
5NV2 2.03 Å, Human DNMT3B PWWP domain in complex with N-isopropyl-1,5-dimethylhexylamine (Metron S)
5NRV 2.08 Å, Human DNMT3B PWWP domain in complex with 6-dipropylamino-1-hexanol
7O45 2.1 Å, Crystal structure of ADD domain of the human DNMT3B methyltransferase
5CIU 2.24 Å, Structural basis of the recognition of H3K36me3 by DNMT3B PWWP domain
6R3E 2.27 Å, Human DNMT3B PWWP domain in complex with triisopropanolamine
5NR3 2.3 Å, Human DNMT3B PWWP domain in complex with ethambutol
5NRS 2.3 Å, Human DNMT3B PWWP domain in complex with N,N-bis(2-hydroxypropyl)ethanolamine
5NV0 2.4 Å, Human DNMT3B PWWP domain in complex with 4-(dipropylamino)butyronitrile
5NVO 2.4 Å, Human DNMT3B PWWP domain in complex with choline
5NV7 2.57 Å, Human DNMT3B PWWP domain in complex with N1-(2-hydroxyethyl)-2-methyl-1,2-propanediamine

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