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M1A58 tRNA methyltransferase mutant - D170A

Analyse M1A58 tRNA methyltransferase mutant - D170A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5C1I
Type: protein
Length: 878 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TRNA (ADENINE(58)-N(1))-methyltransferase trmi
EC: 2.1.1.220
UniProt: Q8GBB2
Ligands: SO4
Pockets: 15 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 31% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	TRNA (ADENINE(58)-N(1))-methyltransferase trmi (EC 2.1.1.220)	protein	220	32% helix, 30% strand	Q8GBB2
B	TRNA (ADENINE(58)-N(1))-methyltransferase trmi (EC 2.1.1.220)	protein	251	28% helix, 34% strand	Q8GBB2
C	TRNA (ADENINE(58)-N(1))-methyltransferase trmi (EC 2.1.1.220)	protein	210	31% helix, 32% strand	Q8GBB2
D	TRNA (ADENINE(58)-N(1))-methyltransferase trmi (EC 2.1.1.220)	protein	197	32% helix, 31% strand	Q8GBB2

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains B, D

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

Pockets

15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	492	0.85	0.92	45	empty
2	154	0.82	0.98	24	empty
3	125	0.79	0.97	25	empty
4	535	0.66	0.77	57	empty
5	341	0.59	0.77	29	empty

Interfaces

6 interfaces between chains.

A–C · 2214 Å² buried · 43 hydrogen bonds · protein-protein
B–D · 2187 Å² buried · 37 hydrogen bonds · protein-protein
A–D · 798 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 756 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 211 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5C1I · m1A58 tRNA methyltransferase mutant - D170A · the same entry in another collection · chain D against D, TM-score 1.00
Q8GBB2 · AlphaFold monomer V2.0 prediction for tRNA (ADENINE(58)-N(1))-methyltransferase trmi… · 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 Q8GBB2
Elsewhere: RCSB PDB 5C1I · PDBe 5C1I · UniProt Q8GBB2

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