MolNFT v1 · #176981 · protein

Crystal structure of sah bound trml from vibrio vulnificus

7E3Q · TRNA (CYTIDINE(34)-2'-O)-methyltransferase: “Crystal structure of sah bound trml from vibrio vulnificus”. X-ray diffraction, 1 ligand (SAH), 4 pockets (best druggability 0.63). MolNFT v1 #176981 on GenesisL1: 3D structure, binding…

PDB: 7E3Q
Type: protein
Length: 318 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TRNA (CYTIDINE(34)-2'-O)-methyltransferase
EC: 2.1.1.207
UniProt: A0A1W6M7K7
Ligands: SAH
Pockets: 4 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	TRNA (CYTIDINE(34)-2'-O)-methyltransferase (EC 2.1.1.207)	protein	159	33% helix, 16% strand	A0A1W6M7K7

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · chains 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	269	0.63	0.81	43	SAH
2	252	0.60	0.80	30	empty
3	53	0.43	0.83	14	empty
4	62	0.41	0.81	15	empty

Interfaces

1 interface between chains.

A–B · 1478 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

7E3Q · Crystal structure of SAH bound TrmL from Vibrio vulnificus · 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 A0A1W6M7K7
Elsewhere: RCSB PDB 7E3Q · PDBe 7E3Q · UniProt A0A1W6M7K7

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