MolNFT v1 · #153024 · protein
Crystal structure of yeast RTT107 and SLX4
6J0Y · Regulator of TY1 transposition protein 107: “Crystal structure of yeast RTT107 and SLX4”. X-ray diffraction, 13 pockets (best druggability 0.84). MolNFT v1 #153024 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6J0Y
- Type
- protein
- Length
- 1,060 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Regulator of TY1 transposition protein 107; Peptide from structure-specific endonuclease…
- UniProt
- P38850, Q12098
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Regulator of TY1 transposition protein 107 | protein | 475 | 39% helix, 15% strand | P38850 |
| C | Peptide from structure-specific endonuclease subunit SLX4 | protein | 58 | 7% helix, 38% strand | Q12098 |
| B | Regulator of TY1 transposition protein 107 | protein | 474 | 38% helix, 14% strand | P38850 |
| D | Peptide from structure-specific endonuclease subunit SLX4 | protein | 53 | 6% helix, 42% strand | Q12098 |
Pockets
13 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.84 | 0.85 | 140 | empty |
| 2 | 601 | 0.82 | 0.87 | 80 | empty |
| 3 | 104 | 0.80 | 0.99 | 17 | empty |
| 4 | 491 | 0.80 | 0.87 | 74 | empty |
| 5 | 99 | 0.79 | 0.98 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1714 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 1580 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 551 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 433 Ų buried · 5 hydrogen bonds · protein-protein
- C–B · 259 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6J0Y · Crystal Structure of Yeast Rtt107 and Slx4 · 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 1.00
- Q12098 · AlphaFold monomer V2.0 prediction for structure-specific endonuclease subunit SLX4… · a predicted model of the same protein · chain D against A, TM-score 0.59
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 Q12098
- Elsewhere: RCSB PDB 6J0Y · PDBe 6J0Y · UniProt P38850 · UniProt Q12098
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