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The nac domain of ANAC019 in complex with DNA, gold derivative

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

PDB: 3SWM
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
Ligands: AU
Pockets: 15 · best druggability 0.70

Structure

x-ray diffraction · 5 distinct chains · 20% 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	24% helix, 44% strand	Q9C932
C	Nac domain-containing protein 19	protein	135	17% helix, 44% strand	Q9C932
E	Oligonucleotide forward	dna	26	—	—
F	Oligonucleotide reverse	dna	26	—	—

Ligands and binding sites

AU · Gold ion · metal · 9 copies · chains A, C, D, B

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

Pockets

15 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	804	0.70	0.76	76	empty
2	187	0.55	0.79	29	empty
3	111	0.51	0.82	19	empty
4	149	0.48	0.77	21	empty
5	141	0.48	0.78	14	empty

Interfaces

10 interfaces between chains.

E–F · 1116 Å² buried · 98 hydrogen bonds · nucleic-nucleic
A–B · 793 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 747 Å² buried · 13 hydrogen bonds · protein-protein
A–E · 469 Å² buried · 12 hydrogen bonds · protein-nucleic
B–F · 461 Å² buried · 10 hydrogen bonds · protein-nucleic

Compared structures

3SWM · The NAC domain of ANAC019 in complex with DNA, gold derivative · 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 C 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 3SWM · PDBe 3SWM · UniProt Q9C932

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