MolNFT v1 · #141735 · protein

Apo crystal structure of trmd from mycobacterium tuberculosis

5ZHI · TRNA (guanine-N(1)-)-methyltransferase: “Apo crystal structure of trmd from mycobacterium tuberculosis”. X-ray diffraction, 3 pockets (best druggability 0.74). MolNFT v1 #141735 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5ZHI
Type: protein
Length: 420 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TRNA (guanine-N(1)-)-methyltransferase
EC: 2.1.1.228
UniProt: P9WFY6
Pockets: 3 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228)	protein	208	40% helix, 22% strand	P9WFY6
B	TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228)	protein	212	39% helix, 21% strand	P9WFY6

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	201	0.74	0.90	40	empty
2	534	0.74	0.82	70	empty
3	83	0.40	0.78	19	empty

Interfaces

1 interface between chains.

A–B · 3709 Å² buried · 70 hydrogen bonds · protein-protein

Compared structures

5ZHI · Apo crystal structure of TrmD from Mycobacterium tuberculosis · the same entry in another collection · chain A against A, TM-score 1.00
P9WFY6 · AlphaFold monomer V2.0 prediction for tRNA (guanine-N(1)-)-methyltransferase (P9WFY6) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P9WFY6
Elsewhere: RCSB PDB 5ZHI · PDBe 5ZHI · UniProt P9WFY6

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