MolNFT v1 · #36107 · protein + DNA
Structure of an NDT80-DNA complex (mse mutant MA9C)
2EVJ · 5'-D(*TP*GP*CP*GP*AP*CP*AP*CP*AP*AP*AP*CP*AP*C)-3': “Structure of an NDT80-DNA complex (mse mutant MA9C)”. X-ray diffraction, 6 pockets (best druggability 0.68). MolNFT v1 #36107 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2EVJ
- 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*AP*AP*AP*CP*AP*C)-3'…
- UniProt
- P38830
- Pockets
- 6 · best druggability 0.68
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*AP*AP*AP*CP*AP*C)-3' | dna | 13 | — | — |
| C | 5'-D(*AP*GP*TP*GP*TP*TP*TP*GP*TP*GP*TP*CP*GP*C)-3' | dna | 14 | — | — |
| A | NDT80 protein | protein | 290 | 16% helix, 41% strand | P38830 |
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 | 201 | 0.68 | 0.87 | 20 | empty |
| 2 | 186 | 0.45 | 0.74 | 29 | empty |
| 3 | 94 | 0.34 | 0.74 | 13 | empty |
| 4 | 60 | 0.33 | 0.77 | 15 | empty |
| 5 | 55 | 0.33 | 0.78 | 12 | empty |
Interfaces
3 interfaces between chains.
- C–A · 819 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–A · 663 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–C · 593 Ų buried · 57 hydrogen bonds · nucleic-nucleic
Compared structures
- 2EVJ · Structure of an Ndt80-DNA complex (MSE mutant mA9C) · 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 2EVJ · PDBe 2EVJ · UniProt P38830
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