Research workbench

Trypanosoma brucei PRMT1 enzyme-prozyme heterotetrameric complex with adohcy

Analyse Trypanosoma brucei PRMT1 enzyme-prozyme heterotetrameric complex with adohcy in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6DNZ
Type: protein
Length: 1,272 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Arginine N-methyltransferase, putative
Ligands: SAH
Pockets: 14 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 25% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Arginine N-methyltransferase, putative	protein	317	26% helix, 39% strand	—
B, D	Arginine N-methyltransferase, putative	protein	319	24% helix, 38% strand	—

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, C
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, C
GOL · Glycerol · additive · 2 copies · chains B, 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, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	280	0.69	0.84	40	SAH
2	477	0.68	0.79	47	empty
3	461	0.67	0.79	44	GOL
4	293	0.67	0.82	39	SAH
5	234	0.61	0.81	36	empty

Interfaces

5 interfaces between chains.

C–D · 1716 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1679 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 507 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 506 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 199 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 36 modified (engineered).

Compared structures

6DNZ · Trypanosoma brucei PRMT1 enzyme-prozyme heterotetrameric complex with AdoHcy · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 6DNZ · PDBe 6DNZ

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