Research workbench
Crystal structure of RIF2 in complex with the C-terminal domain of RAP1 (RAP1-rct)
Analyse Crystal structure of RIF2 in complex with the C-terminal domain of RAP1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BJ5
- Type
- protein
- Length
- 911 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein RIF2; DNA-binding protein RAP1
- UniProt
- Q06208, P11938
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein RIF2 | protein | 292 | 53% helix, 13% strand | Q06208 |
| B | Protein RIF2 | protein | 291 | 52% helix, 13% strand | Q06208 |
| C, E | DNA-binding protein RAP1 | protein | 151 | 59% helix, 3% strand | P11938 |
| D, F | DNA-binding protein RAP1 | protein | 13 | 38% helix, 8% strand | Q06208 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.72 | 0.98 | 18 | empty |
| 2 | 977 | 0.70 | 0.75 | 77 | empty |
| 3 | 75 | 0.68 | 0.93 | 19 | empty |
| 4 | 180 | 0.54 | 0.79 | 31 | empty |
| 5 | 196 | 0.54 | 0.78 | 32 | empty |
Interfaces
5 interfaces between chains.
- B–C · 829 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 743 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 661 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 640 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 460 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4BJ5 · Crystal structure of Rif2 in complex with the C-terminal domain of Rap1 (Rap1-RCT) · the same entry in another collection · chain F against F, TM-score 1.00
- Q06208 · AlphaFold monomer V2.0 prediction for protein RIF2 (Q06208) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P11938 · AlphaFold monomer V2.0 prediction for DNA-binding protein RAP1 (P11938) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 Q06208
- Every structure of UniProt P11938
- Elsewhere: RCSB PDB 4BJ5 · PDBe 4BJ5 · UniProt Q06208 · UniProt P11938
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