MolNFT v1 · #147921 · protein

Structure of human TFB2M

6ERO · Dimethyladenosine transferase 2, mitochondrial…: “Structure of human TFB2M”. X-ray diffraction, 1 ligand (CL), 4 pockets (best druggability 0.72). MolNFT v1 #147921 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6ERO
Type: protein
Length: 573 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dimethyladenosine transferase 2, mitochondrial, dimethyladenosine transferase 2…
EC: 2.1.1.-
UniProt: Q9H5Q4
Ligands: CL
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dimethyladenosine transferase 2, mitochondrial, dimethyladenosine transferase 2, mitochondrial (EC 2.1.1.-)	protein	296	42% helix, 17% strand	Q9H5Q4
B	Dimethyladenosine transferase 2, mitochondrial, dimethyladenosine transferase 2, mitochondrial (EC 2.1.1.-)	protein	277	44% helix, 17% strand	Q9H5Q4

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · chains A
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	777	0.72	0.78	61	empty
2	89	0.44	0.80	15	empty
3	130	0.42	0.75	31	empty
4	62	0.30	0.74	14	empty

Interfaces

1 interface between chains.

A–B · 581 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6ERO · Structure of human TFB2M · the same entry in another collection · chain A against A, TM-score 1.00
Q9H5Q4 · AlphaFold monomer V2.0 prediction for dimethyladenosine transferase 2, mitochondrial… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q9H5Q4
Elsewhere: RCSB PDB 6ERO · PDBe 6ERO · UniProt Q9H5Q4

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