MolNFT v1 · #179882 · protein

Structure of recombinant human DNASE1L3 in complex with MG2+

7KIU · Deoxyribonuclease gamma: “Structure of recombinant human DNASE1L3 in complex with MG2+”. X-ray diffraction, 1 ligand (MG), 9 pockets (best druggability 0.83). MolNFT v1 #179882 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 7KIU
Type: protein
Length: 1,052 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Deoxyribonuclease gamma
EC: 3.1.21.-
UniProt: Q13609
Ligands: MG
Pockets: 9 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 29% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Deoxyribonuclease gamma (EC 3.1.21.-)	protein	263	29% helix, 29% strand	Q13609

Ligands and binding sites

MG · Magnesium ion · metal · 12 copies · chains A, B, C, D

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

Pockets

9 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	1047	0.83	0.84	96	MG
2	1109	0.73	0.77	80	empty
3	473	0.71	0.81	49	empty
4	155	0.52	0.79	26	empty
5	141	0.46	0.77	21	empty

Interfaces

4 interfaces between chains.

A–D · 664 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 645 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 601 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 59 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

7KIU · Structure of recombinant human DNase1L3 in complex with Mg2+ · the same entry in another collection · chain D against D, TM-score 1.00
Q13609 · AlphaFold monomer V2.0 prediction for deoxyribonuclease gamma (Q13609) · a predicted model of the same protein · chain C 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 Q13609
Elsewhere: RCSB PDB 7KIU · PDBe 7KIU · UniProt Q13609

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