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X-ray structure of a C-3'-methyltransferase in complex with S- adenosylmethionine and dtmp

Analyse X-ray structure of a C-3'-methyltransferase in complex with S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3NDI
Type: protein
Length: 405 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methyltransferase
UniProt: B5L6K6
Ligands: SAM, TMP, ZN, PO4
Pockets: 3 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methyltransferase	protein	405	38% helix, 25% strand	B5L6K6

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · chains A
TMP · Thymidine-5'-phosphate · ligand · chains A
ZN · Zinc ion · metal · chains A
PO4 · Phosphate ion · ion · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	348	0.84	0.93	60	SAM, TMP
2	64	0.33	0.76	14	empty
3	50	0.32	0.78	15	empty

Compared structures

3NDI · X-ray Structure of a C-3'-Methyltransferase in Complex with S-adenosylmethionine and dTMP · 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 B5L6K6
Elsewhere: RCSB PDB 3NDI · PDBe 3NDI · UniProt B5L6K6

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