MolNFT v1 · #64406 · protein + DNA

Complex of MTH0212 and a 4 bp dsdna with 3'-overhang

3G2D · Exodeoxyribonuclease: “Complex of MTH0212 and a 4 bp dsdna with 3'-overhang”. X-ray diffraction, 1 ligand (PO4), 8 pockets (best druggability 0.60). MolNFT v1 #64406 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3G2D
Type: protein + DNA
Length: 536 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Exodeoxyribonuclease; 5'-D(*CP*GP*CP*G*CP*AP*GP*GP*C)-3'…
EC: 3.1.11.2
UniProt: O26314
Ligands: PO4
Pockets: 8 · best druggability 0.60

Structure

x-ray diffraction · 5 distinct chains · 32% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Exodeoxyribonuclease (EC 3.1.11.2)	protein	256	32% helix, 27% strand	O26314
B	Exodeoxyribonuclease (EC 3.1.11.2)	protein	255	32% helix, 27% strand	O26314
G, H	5'-D(CPGPCPGCPAPGPGP*C)-3'	dna	4	—	—
K	5'-D(CPCPTPGPUPGPCPGPAPT)-3'	dna	8	—	—
I	5'-D(CPCPTPGPUPGPCPGPAPT)-3'	dna	9	—	—

Ligands and binding sites

PO4 · Phosphate ion · ion · 3 copies · chains A, K, B
GOL · Glycerol · additive · 7 copies · chains A, K, B
PG4 · Tetraethylene glycol · additive · 4 copies · chains A, G, K, 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	222	0.60	0.80	27	PO4
2	116	0.54	0.83	30	PG4
3	114	0.53	0.83	25	empty
4	55	0.44	0.84	15	empty
5	117	0.40	0.75	20	empty

Interfaces

7 interfaces between chains.

A–K · 464 Å² buried · 7 hydrogen bonds · protein-nucleic
B–I · 458 Å² buried · 8 hydrogen bonds · protein-nucleic
B–H · 380 Å² buried · 3 hydrogen bonds · protein-nucleic
A–G · 376 Å² buried · 3 hydrogen bonds · protein-nucleic
A–B · 292 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

3G2D · Complex of Mth0212 and a 4 bp dsDNA with 3'-overhang · the same entry in another collection · chain I against I, 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 3G2D · PDBe 3G2D · UniProt O26314

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