MolNFT v1 · #61282 · protein

Crystal structure of a SAM dependent methyltransferase from aquifex aeolicus

3DH0: “Crystal structure of a SAM dependent methyltransferase from aquifex aeolicus”. X-ray diffraction, 1 ligand (SAM), 3 pockets (best druggability 0.75). MolNFT v1 #61282 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3DH0
Type: protein
Length: 378 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SAM dependent methyltransferase
UniProt: O67440
Ligands: SAM
Pockets: 3 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SAM dependent methyltransferase	protein	188	36% helix, 27% strand	O67440
B	SAM dependent methyltransferase	protein	190	34% helix, 27% strand	O67440

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	295	0.75	0.87	43	SAM
2	253	0.71	0.86	38	SAM
3	275	0.52	0.75	40	empty

Interfaces

1 interface between chains.

A–B · 786 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

3DH0 · Crystal structure of a SAM dependent methyltransferase from Aquifex aeolicus · the same entry in another collection · chain B against B, 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 O67440
Elsewhere: RCSB PDB 3DH0 · PDBe 3DH0 · UniProt O67440

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