MolNFT v1 · #120155 · protein

Crystal structure of trmj from Z. mobilis ZM4

5GRA · TRNA (CYTIDINE/URIDINE-2'-O-)-methyltransferase trmj: “Crystal structure of trmj from Z. mobilis ZM4”. X-ray diffraction, 7 pockets (best druggability 0.76). MolNFT v1 #120155 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5GRA
Type: protein
Length: 447 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TRNA (CYTIDINE/URIDINE-2'-O-)-methyltransferase trmj
EC: 2.1.1.200
UniProt: Q5NN83
Pockets: 7 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	TRNA (CYTIDINE/URIDINE-2'-O-)-methyltransferase trmj (EC 2.1.1.200)	protein	224	48% helix, 14% strand	Q5NN83
B	TRNA (CYTIDINE/URIDINE-2'-O-)-methyltransferase trmj (EC 2.1.1.200)	protein	223	47% helix, 12% strand	Q5NN83

Pockets

7 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	76	0.76	0.97	19	empty
2	82	0.68	0.93	20	empty
3	53	0.49	0.87	17	empty
4	132	0.48	0.79	23	empty
5	186	0.46	0.75	39	empty

Interfaces

1 interface between chains.

A–B · 2220 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

5GRA · Crystal structure of TrmJ from Z. mobilis ZM4 · 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
Every structure of UniProt Q5NN83
Elsewhere: RCSB PDB 5GRA · PDBe 5GRA · UniProt Q5NN83

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