Research workbench

MTH0212 in complex with a short ssdna (cgta)

Analyse MTH0212 in complex with a short ssdna (cgta) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3G2C
Type: protein + DNA
Length: 516 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Exodeoxyribonuclease; 5'-D(P*CP*GP*TP*A)-3'
EC: 3.1.11.2
UniProt: O26314
Ligands: MG, PO4
Pockets: 5 · best druggability 0.56

Structure

x-ray diffraction · 3 distinct chains · 29% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Exodeoxyribonuclease (EC 3.1.11.2)	protein	257	31% helix, 27% strand	O26314
B	Exodeoxyribonuclease (EC 3.1.11.2)	protein	255	27% helix, 27% strand	O26314
I	5'-D(PCPGPTPA)-3'	dna	4	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B
PO4 · Phosphate ion · ion · 3 copies · chains A, B
GOL · Glycerol · additive · 7 copies · chains A, B, I

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	230	0.56	0.78	30	MG, PO4
2	203	0.50	0.77	26	MG, PO4
3	85	0.42	0.79	15	empty
4	73	0.31	0.73	15	empty
5	70	0.30	0.74	18	empty

Interfaces

3 interfaces between chains.

B–I · 467 Å² buried · 10 hydrogen bonds · protein-nucleic
A–I · 243 Å² buried · 2 hydrogen bonds · protein-nucleic
A–B · 68 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3G2C · Mth0212 in complex with a short ssDNA (CGTA) · the same entry in another collection · chain A against A, TM-score 1.00
O26314 · AlphaFold monomer V2.0 prediction for DNA uridine endonuclease (O26314) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 O26314
Elsewhere: RCSB PDB 3G2C · PDBe 3G2C · UniProt O26314

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