MolNFT v1 · #98590 · protein
Crystal structure of the DNA binding domain of a. thailana auxin response factor 1
4LDV: “Crystal structure of the DNA binding domain of a. thailana auxin response factor 1”. X-ray diffraction, 2 ligands (CL, IOD), 6 pockets (best druggability 0.62). MolNFT v1 #98590 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4LDV
- Type
- protein
- Length
- 322 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Auxin response factor 1
- UniProt
- Q8L7G0
- Ligands
- CL, IOD
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Auxin response factor 1 | protein | 322 | 21% helix, 30% strand | Q8L7G0 |
Ligands and binding sites
- CL · Chloride ion · ion · 7 copies · chains A
- IOD · Iodide ion · ion · chains A
- FMT · Formic acid · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.62 | 0.79 | 45 | empty |
| 2 | 79 | 0.37 | 0.76 | 15 | empty |
| 3 | 97 | 0.36 | 0.74 | 24 | CL, FMT |
| 4 | 82 | 0.33 | 0.74 | 19 | empty |
| 5 | 58 | 0.32 | 0.77 | 14 | CL, FMT |
Compared structures
- 4LDV · Crystal structure of the DNA binding domain of A. thailana auxin response factor 1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q8L7G0 · AlphaFold monomer V2.0 prediction for auxin response factor 1 (Q8L7G0) · a predicted model of the same protein · chain A against A, TM-score 0.87
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 Q8L7G0
- Elsewhere: RCSB PDB 4LDV · PDBe 4LDV · UniProt Q8L7G0
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