MolNFT v1 · #86857 · protein
Crystal structure RIF2 in complex with the C-terminal domain of RAP1 (RAP1-rct)
4BJ6 · RAP1-interacting factor 2: “Crystal structure RIF2 in complex with the C-terminal domain of RAP1 (RAP1-rct)”. X-ray diffraction, 1 ligand (SO4), 12 pockets (best druggability 0.72). MolNFT v1 #86857 on GenesisL1: 3D structure…
- PDB
- 4BJ6
- Type
- protein
- Length
- 911 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAP1-interacting factor 2; DNA-binding protein RAP1
- UniProt
- Q06208, P11938
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAP1-interacting factor 2 | protein | 293 | 51% helix, 12% strand | Q06208 |
| B | RAP1-interacting factor 2 | protein | 290 | 50% helix, 12% strand | Q06208 |
| C, E | DNA-binding protein RAP1 | protein | 151 | 58% helix, 3% strand | P11938 |
| D, F | RAP1-interacting factor 2 | protein | 13 | 38% helix, 8% strand | Q06208 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.72 | 0.98 | 18 | empty |
| 2 | 55 | 0.72 | 0.98 | 17 | empty |
| 3 | 1039 | 0.70 | 0.75 | 79 | empty |
| 4 | 169 | 0.52 | 0.79 | 26 | empty |
| 5 | 192 | 0.52 | 0.77 | 30 | empty |
Interfaces
5 interfaces between chains.
- B–C · 787 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 759 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 701 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 681 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 504 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4BJ6 · Crystal structure 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 B 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 4BJ6 · PDBe 4BJ6 · UniProt Q06208 · UniProt P11938
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