Research workbench
Crystal structure of the DNA binding domain of arabidopsis thaliana auxin response factor 1 (ARF1) in complex with protomor-like sequence ER7
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
- 4LDX
- Type
- protein + DNA
- Length
- 711 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Auxin response factor 1; ER7, forward sequence; ER7, reverse sequence
- UniProt
- Q8L7G0
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Auxin response factor 1 | protein | 332 | 21% helix, 30% strand | Q8L7G0 |
| B | Auxin response factor 1 | protein | 337 | 21% helix, 30% strand | Q8L7G0 |
| C | ER7, forward sequence | dna | 21 | — | — |
| D | ER7, reverse sequence | dna | 21 | — | — |
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 957 | 0.79 | 0.81 | 101 | empty |
| 2 | 100 | 0.68 | 0.92 | 25 | empty |
| 3 | 77 | 0.66 | 0.93 | 21 | empty |
| 4 | 343 | 0.64 | 0.80 | 40 | empty |
| 5 | 202 | 0.50 | 0.76 | 34 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1250 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 908 Ų buried · 73 hydrogen bonds · nucleic-nucleic
- A–C · 534 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–D · 514 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–D · 468 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 4LDX · Crystal structure of the DNA binding domain of arabidopsis thaliana auxin response factor… · the same entry in another collection · chain B against B, 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 0.99
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 Q8L7G0
- Elsewhere: RCSB PDB 4LDX · PDBe 4LDX · UniProt Q8L7G0
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