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MTH0212 in complex with a 9BP blunt end dsdna at 1.7 ångström

Analyse MTH0212 in complex with a 9BP blunt end dsdna at 1.7 ångström in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3G00
Type: protein + DNA
Length: 530 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Exodeoxyribonuclease; 5'-D(*CP*GP*TP*AP*TP*TP*AP*CP*G)-3'…
EC: 3.1.11.2
UniProt: O26314
Ligands: PO4
Pockets: 4 · best druggability 0.52

Structure

x-ray diffraction · 4 distinct chains · 30% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Exodeoxyribonuclease (EC 3.1.11.2)	protein	257	30% helix, 27% strand	O26314
B	Exodeoxyribonuclease (EC 3.1.11.2)	protein	255	30% helix, 27% strand	O26314
H	5'-D(CPGPTPAPTPTPAPCP*G)-3'	dna	9	—	—
I	5'-D(CPGPTPAPUPTPAPCP*G)-3'	dna	9	—	—

Ligands and binding sites

PO4 · Phosphate ion · ion · 4 copies · chains A, I, B, H
GOL · Glycerol · additive · 3 copies · chains A, I, B
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B, H

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

Pockets

4 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	116	0.52	0.82	33	PO4
2	104	0.51	0.82	33	PO4
3	54	0.47	0.86	17	empty
4	92	0.31	0.73	11	empty

Interfaces

5 interfaces between chains.

B–I · 497 Å² buried · 9 hydrogen bonds · protein-nucleic
A–H · 490 Å² buried · 10 hydrogen bonds · protein-nucleic
H–I · 428 Å² buried · 38 hydrogen bonds · nucleic-nucleic
A–I · 378 Å² buried · 5 hydrogen bonds · protein-nucleic
B–H · 376 Å² buried · 5 hydrogen bonds · protein-nucleic

Compared structures

3G00 · Mth0212 in complex with a 9bp blunt end dsDNA at 1.7 Angstrom · 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 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 O26314
Elsewhere: RCSB PDB 3G00 · PDBe 3G00 · UniProt O26314

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