Research workbench

ANAC019 nac domain in complex with DNA

Analyse ANAC019 nac domain in complex with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3SWP
Type: protein + DNA
Length: 608 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nac domain-containing protein 19; Oligonucleotide forward; Oligonucleotide reverse
UniProt: Q9C932
Pockets: 13 · best druggability 0.62

Structure

x-ray diffraction · 5 distinct chains · 18% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nac domain-containing protein 19	protein	141	18% helix, 43% strand	Q9C932
B, D	Nac domain-containing protein 19	protein	140	18% helix, 43% strand	Q9C932
C	Nac domain-containing protein 19	protein	135	17% helix, 45% strand	Q9C932
E	Oligonucleotide forward	dna	26	—	—
F	Oligonucleotide reverse	dna	26	—	—

Pockets

13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	594	0.62	0.75	47	empty
2	258	0.59	0.79	31	empty
3	205	0.59	0.80	23	empty
4	421	0.58	0.75	42	empty
5	234	0.55	0.78	26	empty

Interfaces

11 interfaces between chains.

E–F · 1158 Å² buried · 93 hydrogen bonds · nucleic-nucleic
A–B · 731 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 678 Å² buried · 15 hydrogen bonds · protein-protein
A–E · 489 Å² buried · 12 hydrogen bonds · protein-nucleic
B–F · 417 Å² buried · 1 hydrogen bond · protein-nucleic

Compared structures

3SWP · ANAC019 NAC domain in complex with DNA · the same entry in another collection · chain F against F, TM-score 1.00
Q9C932 · AlphaFold monomer V2.0 prediction for nac domain-containing protein 19 (Q9C932) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 Q9C932
Elsewhere: RCSB PDB 3SWP · PDBe 3SWP · UniProt Q9C932

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