Research workbench
Crystal structure of a novel DNA-binding domain from NDT80, a transcriptional activator required for meiosis in yeast
Analyse Crystal structure of a novel DNA-binding domain from NDT80, a transcriptional… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1M6U
- Type
- protein
- Length
- 515 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NDT80 protein
- UniProt
- P38830
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NDT80 protein | protein | 265 | 13% helix, 42% strand | P38830 |
| B | NDT80 protein | protein | 250 | 12% helix, 41% strand | P38830 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.71 | 0.75 | 96 | empty |
| 2 | 250 | 0.49 | 0.74 | 35 | SO4 |
| 3 | 86 | 0.31 | 0.73 | 16 | empty |
| 4 | 50 | 0.30 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 470 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1M6U · Crystal Structure of a Novel DNA-binding domain from Ndt80, a Transcriptional Activator… · the same entry in another collection · chain A against A, TM-score 1.00
- P38830 · AlphaFold monomer V2.0 prediction for meiosis-specific transcription factor NDT80 (P38830) · a predicted model of the same protein · chain B 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 P38830
- Elsewhere: RCSB PDB 1M6U · PDBe 1M6U · UniProt P38830
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