MolNFT v1 · #31245 · protein + DNA

Crystal structure of muth-hemimethylated DNA complex

2AOR · 5'-D(*CP*AP*GP*GP*(6MA) P*TP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*A…: “Crystal structure of muth-hemimethylated DNA complex”. X-ray diffraction, 1 ligand (CA), 8 pockets (best druggability 0.58). MolNFT v1 #31245 on GenesisL1: 3D…

PDB: 2AOR
Type: protein + DNA
Length: 485 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*CP*AP*GP*GP*(6MA) P*TP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*AP*TP*CP*CP*TP*G)-3'; DNA…
UniProt: P44688
Ligands: CA
Pockets: 8 · best druggability 0.58

Structure

x-ray diffraction · 3 distinct chains · 33% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, D	5'-D(CPAPGPGP(6MA) PTPCPCPAPAPGPCPTPTPGPGPAPTPCPCPTPG)-3'	dna	22	—	—
A	DNA mismatch repair protein muth	protein	220	32% helix, 21% strand	P44688
B	DNA mismatch repair protein muth	protein	221	33% helix, 21% strand	P44688

Ligands and binding sites

CA · Calcium ion · metal · 4 copies · chains D, A, C, B

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

Pockets

8 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	111	0.58	0.85	29	CA
2	341	0.57	0.76	36	empty
3	247	0.52	0.76	28	empty
4	207	0.52	0.77	32	empty
5	142	0.43	0.76	25	empty

Interfaces

6 interfaces between chains.

C–D · 1012 Å² buried · 92 hydrogen bonds · nucleic-nucleic
C–B · 948 Å² buried · 14 hydrogen bonds · protein-nucleic
D–A · 939 Å² buried · 14 hydrogen bonds · protein-nucleic
C–A · 920 Å² buried · 13 hydrogen bonds · protein-nucleic
D–B · 896 Å² buried · 14 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

2AOR · Crystal structure of MutH-hemimethylated DNA complex · the same entry in another collection · chain C against C, TM-score 1.00
P44688 · AlphaFold monomer V2.0 prediction for DNA mismatch repair protein muth (P44688) · 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 P44688
Elsewhere: RCSB PDB 2AOR · PDBe 2AOR · UniProt P44688

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