Research workbench
Crystal structure of the RIF1 N-terminal domain (RIF1-ntd) from saccharomyces cerevisiae in complex with DNA
Analyse Crystal structure of the RIF1 N-terminal domain (RIF1-ntd) from saccharomyces… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NW5
- Type
- protein + DNA
- Length
- 2,230 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Telomere length regulator protein RIF1; DNA (60-mer); DNA (30-mer)
- UniProt
- P29539
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Telomere length regulator protein RIF1 | protein | 1085 | 68% helix, 0% strand | P29539 |
| B | Telomere length regulator protein RIF1 | protein | 1085 | 68% helix, 0% strand | P29539 |
| C | DNA (60-mer) | dna | 30 | — | — |
| D | DNA (30-mer) | dna | 30 | — | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.82 | 0.95 | 31 | empty |
| 2 | 671 | 0.82 | 0.85 | 52 | empty |
| 3 | 193 | 0.80 | 0.94 | 32 | empty |
| 4 | 460 | 0.80 | 0.87 | 57 | empty |
| 5 | 275 | 0.78 | 0.90 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1512 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1336 Ų buried · 84 hydrogen bonds · nucleic-nucleic
- B–C · 245 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–C · 195 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–D · 137 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 5NW5 · Crystal structure of the Rif1 N-terminal domain (RIF1-NTD) from Saccharomyces cerevisiae… · the same entry in another collection · chain A against A, TM-score 1.00
- P29539 · AlphaFold monomer V2.0 prediction for telomere length regulator protein RIF1 (P29539) · a predicted model of the same protein · chain A against A, TM-score 0.85
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 P29539
- Elsewhere: RCSB PDB 5NW5 · PDBe 5NW5 · UniProt P29539
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