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Structure of E. COLI DNA adenine methyltransferase (dam)

Analyse Structure of E. COLI DNA adenine methyltransferase (dam) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2G1P
Type: protein + DNA
Length: 514 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*TP*CP*TP*AP*GP*AP*TP*CP*TP*AP*GP*A)-3'; DNA adenine methylase
EC: 2.1.1.72
UniProt: P0AEE8
Ligands: SAH
Pockets: 3 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
F, G	5'-D(TPCPTPAPGPAPTPCPTPAPGPA)-3'	dna	12	—	—
A	DNA adenine methylase (EC 2.1.1.72)	protein	244	44% helix, 17% strand	P0AEE8
B	DNA adenine methylase (EC 2.1.1.72)	protein	246	44% helix, 17% strand	P0AEE8

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
GOL · Glycerol · additive · chains 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	998	0.73	0.76	61	SAH, GOL
2	602	0.68	0.77	47	SAH
3	368	0.55	0.74	32	empty

Interfaces

5 interfaces between chains.

F–A · 640 Å² buried · 12 hydrogen bonds · protein-nucleic
G–A · 535 Å² buried · 12 hydrogen bonds · protein-nucleic
G–B · 481 Å² buried · 13 hydrogen bonds · protein-nucleic
F–G · 450 Å² buried · 32 hydrogen bonds · nucleic-nucleic
F–B · 75 Å² buried · 0 hydrogen bonds · protein-nucleic

Compared structures

2G1P · Structure of E. coli DNA adenine methyltransferase (DAM) · the same entry in another collection · chain F against F, TM-score 1.00
P0AEE8 · AlphaFold monomer V2.0 prediction for DNA adenine methylase (P0AEE8) · a predicted model of the same protein · 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 P0AEE8
Elsewhere: RCSB PDB 2G1P · PDBe 2G1P · UniProt P0AEE8

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