Research workbench
Structure of a NDT80-DNA complex (mse mutant MA6T)
Analyse Structure of a NDT80-DNA complex (mse mutant MA6T) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EVF
- Type
- protein + DNA
- Length
- 317 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*GP*CP*GP*AP*CP*AP*CP*TP*AP*AP*AP*AP*C)-3'…
- UniProt
- P38830
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*TP*GP*CP*GP*AP*CP*AP*CP*TP*AP*AP*AP*AP*C)-3' | dna | 13 | — | — |
| C | 5'-D(*AP*GP*TP*TP*TP*TP*AP*GP*TP*GP*TP*CP*GP*C)-3' | dna | 14 | — | — |
| A | NDT80 protein | protein | 290 | 16% helix, 41% strand | P38830 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.70 | 0.88 | 22 | empty |
| 2 | 206 | 0.48 | 0.75 | 29 | empty |
| 3 | 134 | 0.45 | 0.77 | 29 | empty |
| 4 | 88 | 0.36 | 0.75 | 12 | empty |
| 5 | 55 | 0.29 | 0.76 | 12 | empty |
Interfaces
3 interfaces between chains.
- C–A · 816 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–A · 683 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–C · 583 Ų buried · 46 hydrogen bonds · nucleic-nucleic
Compared structures
- 2EVF · Structure of a Ndt80-DNA complex (MSE mutant mA6T) · the same entry in another collection · chain B against B, 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 A against A, TM-score 1.00
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 2EVF · PDBe 2EVF · UniProt P38830
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