5NRV: Human DNMT3B PWWP domain

Name: PDB 5NRV: Human DNMT3B PWWP domain in complex with 6-dipropylamino-1-hexanol
Published: 2018-06-13
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Human DNMT3B PWWP domain in complex with 6-dipropylamino-1-hexanol. Determined by X-ray diffraction at 2.08 Å resolution. Released 13 Jun 2018.

Method: X-ray diffraction
Resolution: 2.08 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,348
Mol. weight: 34.76 kDa
Ligands: 96K
Released: 13 Jun 2018

Explore 5NRV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5NRV contains 16 α-helices and 10 β-strands across 2 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: 8 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	228-231	4	2
β-strand	239-244	6	2
α-helix	246-249	4
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	296-312	17
α-helix	325-337	13
α-helix	345-348	4

Chain D: 8 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	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 3B	A, D	protein	150	Homo sapiens	Q9UBC3 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>5NRV_1 DNA (cytosine-5)-methyltransferase 3B (chains A, D)
EADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFG
DGKFSEVSADKLVALGLFSQHFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDSL
EDQLKPMLEWAHGGFKPTGIEGLKPNNTQP

Ligands and cofactors

ID	Name	Formula	Copies
96K	6-dipropylamino-1-hexanol	C12 H27 N O	2

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

Primary citation

Targeting PWWP domain of DNA methyltransferase 3B for epigenetic cancer therapy: Identification and structural characterization of new potential protein-protein interaction inhibitors. Rondelet, G., Dal Maso, T., Maniquet, A. et al. To be published.

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)
3QKJ 2.04 Å, The PWWP domain of human DNA (CYTOSINE-5-)-METHYLTRANSFERASE 3 BETA in complex with a…
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

Browse structure collections

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