Research workbench
Crystal structure of LEU3 DNA-binding domain complexed with a 12MER DNA duplex
Analyse Crystal structure of LEU3 DNA-binding domain complexed with a 12MER DNA duplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ER8
- Type
- protein + DNA
- Length
- 315 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*G)-3'; Regulatory protein LEU3
- UniProt
- P08638
- Ligands
- ZN
- Pockets
- 8 · best druggability 0.55
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F, G, H | 5'-D(*CP*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*G)-3' | dna | 12 | — | — |
| A, D | Regulatory protein LEU3 | protein | 68 | 49% helix, 0% strand | P08638 |
| B | Regulatory protein LEU3 | protein | 67 | 51% helix, 0% strand | P08638 |
| C | Regulatory protein LEU3 | protein | 64 | 41% helix, 0% strand | P08638 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.55 | 0.75 | 26 | empty |
| 2 | 302 | 0.52 | 0.74 | 30 | empty |
| 3 | 117 | 0.47 | 0.79 | 14 | empty |
| 4 | 115 | 0.46 | 0.79 | 15 | empty |
| 5 | 92 | 0.46 | 0.81 | 13 | empty |
Interfaces
11 interfaces between chains.
- E–F · 556 Ų buried · 48 hydrogen bonds · nucleic-nucleic
- G–H · 555 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- F–A · 496 Ų buried · 13 hydrogen bonds · protein-nucleic
- G–D · 439 Ų buried · 12 hydrogen bonds · protein-nucleic
- E–B · 421 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 2ER8 · Crystal Structure of Leu3 DNA-binding domain complexed with a 12mer DNA duplex · the same entry in another collection · chain D against D, TM-score 1.00
- P08638 · AlphaFold monomer V2.0 prediction for regulatory protein LEU3 (P08638) · a predicted model of the same protein · chain B against A, TM-score 0.83
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 P08638
- Elsewhere: RCSB PDB 2ER8 · PDBe 2ER8 · UniProt P08638
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