MolNFT v1 · #149489 · protein

Crystal structure of human mitochondrial 5'(3')-deoxyribonucleotidase in complex with the inhibitor pb-peu

6G22 · 5'(3')-deoxyribonucleotidase, mitochondrial: “Crystal structure of human mitochondrial 5'(3')-deoxyribonucleotidase in complex with the inhibitor pb-peu”. X-ray diffraction, 2 ligands (2O2, MG), 2 pockets (best druggability 0.71).…

PDB: 6G22
Type: protein
Length: 193 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'(3')-deoxyribonucleotidase, mitochondrial
EC: 3.1.3.-
UniProt: Q9NPB1
Ligands: 2O2, MG
Pockets: 2 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5'(3')-deoxyribonucleotidase, mitochondrial (EC 3.1.3.-)	protein	193	36% helix, 16% strand	Q9NPB1

Ligands and binding sites

2O2 · 1-{2-deoxy-3,5-O-[phenyl(phosphono)methylidene]-beta-D-threo-pentofuranosyl}-5-[(E)-2-phosphonoethenyl]pyrimidine-2,4(1H,3H)-dione · ligand · chains A
MG · Magnesium ion · metal · chains A
GOL · Glycerol · additive · 2 copies · chains A
BME · Beta-mercaptoethanol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	322	0.71	0.83	32	2O2
2	69	0.34	0.76	16	empty

Modifications

Observed in the structure: 1 covalent (additive adduct).

Compared structures

6G22 · Crystal structure of human mitochondrial 5'(3')-deoxyribonucleotidase in complex with the… · the same entry in another collection · chain A against A, TM-score 1.00
Q9NPB1 · AlphaFold monomer V2.0 prediction for 5'(3')-deoxyribonucleotidase, mitochondrial (Q9NPB1) · a predicted model of the same protein · chain A 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 Q9NPB1
Elsewhere: RCSB PDB 6G22 · PDBe 6G22 · UniProt Q9NPB1

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.