Research workbench

Cytosine-specific methyltransferase HHAI/DNA complex

Analyse Cytosine-specific methyltransferase HHAI/DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8MHT
Type: protein + DNA
Length: 351 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(P*GP*TP*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)-3'…
EC: 2.1.1.73
UniProt: P05102
Ligands: SAH
Pockets: 5 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 30% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	5'-D(PGPTPCPAPGPCPGPCPAPTPGPG)-3'	dna	12	—	—
D	5'-D(PCPCPAPTPGPUPGPCPTPGPAPC)-3'	dna	12	—	—
A	Cytosine-specific methyltransferase hhai (EC 2.1.1.73)	protein	327	30% helix, 18% strand	P05102

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · chains D, A

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

Pockets

5 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	68	0.74	0.99	20	empty
2	331	0.73	0.85	37	SAH
3	220	0.59	0.81	23	empty
4	222	0.57	0.79	32	empty
5	89	0.35	0.76	14	empty

Interfaces

3 interfaces between chains.

D–A · 1018 Å² buried · 27 hydrogen bonds · protein-nucleic
C–A · 664 Å² buried · 11 hydrogen bonds · protein-nucleic
C–D · 561 Å² buried · 41 hydrogen bonds · nucleic-nucleic

Compared structures

8MHT · Cytosine-specific methyltransferase HHAI/DNA complex · the same entry in another collection · chain C against C, TM-score 1.00
P05102 · AlphaFold monomer V2.0 prediction for modification methylase hhai (P05102) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P05102
Elsewhere: RCSB PDB 8MHT · PDBe 8MHT · UniProt P05102

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