MolNFT v1 · #70479 · protein

Crystal structure of the pwwp domain of human DNA (cytosine-5-)- methyltransferase 3 alpha

3LLR · DNA (cytosine-5)-methyltransferase 3A: “Crystal structure of the pwwp domain of human DNA (cytosine-5-)- methyltransferase 3 alpha”. X-ray diffraction, 1 ligand (SO4), 14 pockets (best druggability 0.72). MolNFT v1 #70479 on…

PDB: 3LLR
Type: protein
Length: 670 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (cytosine-5)-methyltransferase 3A
EC: 2.1.1.37
UniProt: Q9Y6K1
Ligands: SO4
Pockets: 14 · best druggability 0.72

Structure

x-ray diffraction · 5 distinct chains · 40% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37)	protein	131	41% helix, 18% strand	Q9Y6K1
B	DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37)	protein	132	39% helix, 18% strand	Q9Y6K1
C	DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37)	protein	131	40% helix, 18% strand	Q9Y6K1
D	DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37)	protein	143	39% helix, 17% strand	Q9Y6K1
E	DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37)	protein	133	42% helix, 20% strand	Q9Y6K1

Ligands and binding sites

SO4 · Sulfate ion · ion · chains B
BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 5 copies · chains A, B, C, E, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	965	0.72	0.76	82	BTB
2	238	0.65	0.83	29	empty
3	211	0.57	0.79	26	empty
4	168	0.56	0.81	21	empty
5	152	0.55	0.81	32	empty

Interfaces

5 interfaces between chains.

B–D · 895 Å² buried · 12 hydrogen bonds · protein-protein
A–E · 677 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 570 Å² buried · 10 hydrogen bonds · protein-protein
C–E · 383 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 105 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3LLR · Crystal structure of the PWWP domain of Human DNA (cytosine-5-)-methyltransferase 3 alpha · the same entry in another collection · chain E against E, TM-score 1.00
Q9Y6K1 · AlphaFold monomer V2.0 prediction for DNA (cytosine-5)-methyltransferase 3A (Q9Y6K1) · a predicted model of the same protein · chain A against A, TM-score 0.98

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9Y6K1
Elsewhere: RCSB PDB 3LLR · PDBe 3LLR · UniProt Q9Y6K1

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