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Crystal structure of the DNA binding domain of arabidopsis thaliana auxin response factor 5

Analyse Crystal structure of the DNA binding domain of arabidopsis thaliana auxin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4LDU
Type: protein
Length: 336 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Auxin response factor 5
UniProt: P93024
Ligands: CL
Pockets: 5 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 22% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Auxin response factor 5	protein	336	22% helix, 30% strand	P93024

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · chains A

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

Pockets

5 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	419	0.63	0.77	41	empty
2	181	0.47	0.76	28	empty
3	94	0.45	0.79	19	CL
4	152	0.41	0.73	27	empty
5	59	0.30	0.75	18	empty

Compared structures

4LDU · Crystal structure of the DNA binding domain of Arabidopsis thaliana auxin response factor… · the same entry in another collection · chain A against A, TM-score 1.00
P93024 · AlphaFold monomer V2.0 prediction for auxin response factor 5 (P93024) · 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 P93024
Elsewhere: RCSB PDB 4LDU · PDBe 4LDU · UniProt P93024

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