MolNFT v1 · #1176 · protein

Atomic structure of the ACTIN:DNASE I complex

1ATN: “Atomic structure of the ACTIN:DNASE I complex”. X-ray diffraction, 5 ligands (ACE, ATP, NAG), 3 pockets (best druggability 0.71). MolNFT v1 #1176 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1ATN
Type: protein
Length: 630 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Actin; Deoxyribonuclease I
UniProt: P02568, P00639
Ligands: ACE, ATP, NAG, BMA, CA
Pockets: 3 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Actin	protein	372	42% helix, 21% strand	P02568
D	Deoxyribonuclease I	protein	258	28% helix, 29% strand	P00639

Ligands and binding sites

ACE · Acetyl group · ligand · chains A
ATP · Adenosine-5'-triphosphate · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains D
BMA · beta-D-mannopyranose · sugar
CA · Calcium ion · metal · 4 copies · chains A, D

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

Pockets

3 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	466	0.71	0.82	53	CA, ATP
2	171	0.47	0.76	31	empty
3	106	0.37	0.74	18	empty

Interfaces

1 interface between chains.

A–D · 917 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide, 1 covalent, 1 glycan, 1 modified (disulfide, covalent ligand, N-glycosylation, methylation).

Compared structures

1ATN · Atomic structure of the actin:DNASE I complex · the same entry in another collection · chain A against A, TM-score 1.00
P00639 · AlphaFold monomer V2.0 prediction for deoxyribonuclease-1 (P00639) · a predicted model of the same protein · chain D 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 P02568
Every structure of UniProt P00639
Elsewhere: RCSB PDB 1ATN · PDBe 1ATN · UniProt P02568 · UniProt P00639

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