3LLR: DNA-methyltransferase 3A

Name: PDB 3LLR: Crystal structure of the PWWP domain of Human DNA (cytosine-5-)-methyltransferase 3 alpha
Published: 2010-03-23
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Crystal structure of the PWWP domain of Human DNA (cytosine-5-)-methyltransferase 3 alpha. Determined by X-ray diffraction at 2.3 Å resolution. Released 23 Mar 2010.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 5
Atoms: 5,810
Mol. weight: 87.44 kDa
Ligands: BTB
Released: 23 Mar 2010

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

Secondary structure: helices and β-sheets

3LLR contains 44 α-helices and 25 β-strands across 5 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: 9 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	21-24	4	1
β-strand	32-37	6	1
α-helix	39-41	3
α-helix	46-48	3
β-strand	51-56	6	1
β-strand	62-66	5	1
α-helix	67-69	3
β-strand	70-72	3	1
α-helix	73-75	3
α-helix	76-79	4
α-helix	82-87	6
α-helix	89-106	18
α-helix	125-137	13
α-helix	145-148	4

Chain B: 8 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	21-24	4	2
β-strand	32-37	6	2
α-helix	39-41	3
α-helix	46-48	3
β-strand	51-56	6	2
β-strand	62-66	5	2
α-helix	67-69	3
β-strand	70-72	3	2
α-helix	76-79	4
α-helix	82-87	6
α-helix	89-106	18
α-helix	125-137	13
α-helix	145-148	4

Chain C: 8 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	21-24	4	3
β-strand	32-37	6	3
α-helix	39-41	3
α-helix	46-48	3
β-strand	51-56	6	3
β-strand	62-66	5	3
α-helix	67-69	3
β-strand	70-72	3	3
α-helix	76-79	4
α-helix	82-87	6
α-helix	89-106	18
α-helix	124-137	14
α-helix	145-148	4

Chain D: 9 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	21-24	4	4
β-strand	32-37	6	4
α-helix	39-41	3
α-helix	45-48	4
β-strand	51-56	6	4
β-strand	62-66	5	4
α-helix	67-69	3
β-strand	70-72	3	4
α-helix	76-79	4
α-helix	82-87	6
α-helix	89-106	18
α-helix	119-121	3
α-helix	124-137	14
α-helix	144-148	5

Chain E: 10 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	21-25	5	5
α-helix	30	1
β-strand	31-37	7	5
α-helix	39-41	3
α-helix	46-48	3
β-strand	51-56	6	5
β-strand	62-66	5	5
α-helix	67-69	3
β-strand	70-72	3	5
α-helix	73-75	3
α-helix	76-79	4
α-helix	82-87	6
α-helix	89-106	18
α-helix	123-137	15
α-helix	145-148	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (cytosine-5)-methyltransferase 3A	A, B, C, D, E	protein	154	Homo sapiens	Q9Y6K1 (AlphaFold model)

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

>3LLR_1 DNA (cytosine-5)-methyltransferase 3A (chains A, B, C, D, E)
GTKAGDDEPEYEDGRGFGIGELVWGKLRGFSWWPGRIVSWWMTGRSRAAEGTRWVMWFGD
GKFSVVCVEKLMPLSSFCSAFHQATYNKQPMYRKAIYEVLQVASSRAGKLFPVCHDSDES
DTAKAVEVQNKPMIEWALGGFQPSGPKGLEPPEE

Ligands and cofactors

ID	Name	Formula	Copies
BTB	2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol	C8 H19 N O5	5

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 Q9Y6K1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8BA5 1.45 Å, Crystal structure of the DNMT3A ADD domain
4QBS 1.8 Å, Crystal structure of DNMT3a ADD domain E545R mutant bound to H3T3ph peptide
4QBR 1.9 Å, Crystal structure of DNMT3a ADD domain G550D mutant bound to H3 peptide
3A1B 2.29 Å, Crystal structure of the DNMT3A ADD domain in complex with histone H3
3A1A 2.3 Å, Crystal Structure of the DNMT3A ADD domain
3SVM 2.31 Å, Human MPP8 - human DNMT3AK47me2 peptide
6W8B 2.4 Å, Structure of DNMT3A in complex with CGA DNA
4QBQ 2.41 Å, Crystal structure of DNMT3a ADD domain bound to H3 peptide
6W8J 2.44 Å, Structure of DNMT3A (R882H) in complex with CAG DNA
8TE1 2.48 Å, Crystal structure of the methyltransferase domain of R882H/R676K DNMT3A homotetramer
6W89 2.5 Å, Structure of DNMT3A (R882H) in complex with CGA DNA
6W8D 2.6 Å, Structure of DNMT3A (R882H) in complex with CGT DNA

Browse structure collections

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