MolNFT v1 · #70211 · protein

The crystal structure of a possible methylase from clostridium difficile 630.

3LDU · Putative methylase: “The crystal structure of a possible methylase from clostridium difficile 630.”. X-ray diffraction, 1 ligand (GTP), 3 pockets (best druggability 0.55). MolNFT v1 #70211 on GenesisL1: 3D structure, binding sites…

PDB: 3LDU
Type: protein
Length: 377 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative methylase
UniProt: Q186Y7
Ligands: GTP
Pockets: 3 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative methylase	protein	377	34% helix, 23% strand	Q186Y7

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · chains A
GOL · Glycerol · additive · 9 copies · chains A
FMT · Formic acid · additive · 2 copies · chains A

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

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	237	0.55	0.78	35	GTP
2	230	0.53	0.77	31	GOL
3	87	0.38	0.76	12	GOL

Modifications

Observed in the structure: 7 modified (engineered).

Compared structures

3LDU · The crystal structure of a possible methylase from Clostridium difficile 630. · 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 Q186Y7
Elsewhere: RCSB PDB 3LDU · PDBe 3LDU · UniProt Q186Y7

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