MolNFT v1 · #148416 · protein

Complex between the haloferax volcanii TRM112 methyltransferase activator and the HVO_0019 putative methyltransferase

6F5Z · 24-sterol C-methyltransferase: “Complex between the haloferax volcanii TRM112 methyltransferase activator and the HVO_0019 putative…”. X-ray diffraction, 1 ligand (SAH), 6 pockets (best druggability 0.72). MolNFT v1 #148416 on…

PDB: 6F5Z
Type: protein
Length: 568 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 24-sterol C-methyltransferase; UPF0434 family protein
UniProt: L9UJ72, D4GW82
Ligands: SAH
Pockets: 6 · best druggability 0.72

Structure

x-ray diffraction · 4 distinct chains · 35% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	24-sterol C-methyltransferase	protein	226	41% helix, 23% strand	L9UJ72
B	24-sterol C-methyltransferase	protein	228	41% helix, 23% strand	L9UJ72
C	UPF0434 family protein	protein	59	15% helix, 47% strand	D4GW82
D	UPF0434 family protein	protein	55	11% helix, 40% strand	D4GW82

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains B, C

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	412	0.72	0.82	58	SAH
2	265	0.68	0.83	42	SAH
3	275	0.61	0.79	29	empty
4	266	0.53	0.76	30	empty
5	90	0.35	0.75	17	empty

Interfaces

3 interfaces between chains.

B–D · 1019 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 1006 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 871 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

6F5Z · Complex between the Haloferax volcanii Trm112 methyltransferase activator and the… · 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 L9UJ72
Every structure of UniProt D4GW82
Elsewhere: RCSB PDB 6F5Z · PDBe 6F5Z · UniProt L9UJ72 · UniProt D4GW82

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