MolNFT v1 · #191587 · protein + DNA

Cytosine-specific methyltransferase HHAI/DNA complex

9MHT · 5'-D(P*CP*CP*AP*TP*GP*CP*GP*CP*TP*GP*AP*C)-3': “Cytosine-specific methyltransferase HHAI/DNA complex”. X-ray diffraction, 1 ligand (SAH), 5 pockets (best druggability 0.76). MolNFT v1 #191587 on GenesisL1: 3D structure, binding…

PDB: 9MHT
Type: protein + DNA
Length: 351 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(P*CP*CP*AP*TP*GP*CP*GP*CP*TP*GP*AP*C)-3'…
EC: 2.1.1.73
UniProt: P05102
Ligands: SAH
Pockets: 5 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 33% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	5'-D(PCPCPAPTPGPCPGPCPTPGPAPC)-3'	dna	12	—	—
D	5'-D(PGPTPCPAPGP(3DR)PGPCPAPTPGPG)- 3'	dna	12	—	—
A	Cytosine-specific methyltransferase hhai (EC 2.1.1.73)	protein	327	33% helix, 18% strand	P05102

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · chains 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	87	0.76	0.98	24	empty
2	348	0.75	0.86	39	SAH
3	270	0.58	0.78	27	empty
4	163	0.56	0.82	18	empty
5	82	0.34	0.75	13	empty

Interfaces

3 interfaces between chains.

D–A · 927 Å² buried · 21 hydrogen bonds · protein-nucleic
C–A · 689 Å² buried · 11 hydrogen bonds · protein-nucleic
C–D · 558 Å² buried · 41 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

9MHT · 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 9MHT · PDBe 9MHT · UniProt P05102

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