MolNFT v1 · #153022 · protein
Crystal structure of yeast RTT107 and NSE6
6J0W · Regulator of TY1 transposition protein 107: “Crystal structure of yeast RTT107 and NSE6”. X-ray diffraction, 14 pockets (best druggability 0.83). MolNFT v1 #153022 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6J0W
- Type
- protein
- Length
- 968 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Regulator of TY1 transposition protein 107; Peptide from DNA repair protein KRE29
- UniProt
- P38850, P40026
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Regulator of TY1 transposition protein 107 | protein | 460 | 38% helix, 14% strand | P38850 |
| B | Regulator of TY1 transposition protein 107 | protein | 457 | 40% helix, 14% strand | P38850 |
| C | Peptide from DNA repair protein KRE29 | protein | 22 | 0% helix, 18% strand | P40026 |
| D | Peptide from DNA repair protein KRE29 | protein | 29 | 0% helix, 7% strand | P40026 |
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.83 | 0.84 | 106 | empty |
| 2 | 152 | 0.78 | 0.95 | 40 | empty |
| 3 | 93 | 0.78 | 0.98 | 18 | empty |
| 4 | 79 | 0.77 | 0.99 | 17 | empty |
| 5 | 57 | 0.69 | 0.97 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1664 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1314 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 928 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6J0W · Crystal Structure of Yeast Rtt107 and Nse6 · the same entry in another collection · chain D against D, TM-score 1.00
- P38850 · AlphaFold monomer V2.0 prediction for regulator of TY1 transposition protein 107 (P38850) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P40026 · AlphaFold monomer V2.0 prediction for DNA repair protein KRE29 (P40026) · a predicted model of the same protein · chain D against A, TM-score 0.24
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 P38850
- Every structure of UniProt P40026
- Elsewhere: RCSB PDB 6J0W · PDBe 6J0W · UniProt P38850 · UniProt P40026
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