Research workbench
RIX1-REA1 pre-60S particle - RIX1-subcomplex, body 3 (rigid body refinement)
Analyse RIX1-REA1 pre-60S particle - RIX1-subcomplex, body 3 (rigid body refinement) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YLE
- Type
- protein
- Length
- 1,930 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pre-rRNA-processing protein IPI3; Pre-rRNA-processing protein RIX1; Pre-rRNA-processing…
- UniProt
- P53877, P38883, A6ZSZ4
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 5 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pre-rRNA-processing protein IPI3 | protein | 399 | 5% helix, 44% strand | P53877 |
| B | Pre-rRNA-processing protein IPI3 | protein | 415 | 5% helix, 41% strand | P53877 |
| C | Pre-rRNA-processing protein RIX1 | protein | 545 | 63% helix, 2% strand | P38883 |
| D | Pre-rRNA-processing protein RIX1 | protein | 547 | 65% helix, 2% strand | P38883 |
| K | Pre-rRNA-processing protein IPI1 | protein | 24 | 0% helix, 0% strand | A6ZSZ4 |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.87 | 0.89 | 119 | empty |
| 2 | 1085 | 0.85 | 0.86 | 102 | empty |
| 3 | 852 | 0.83 | 0.85 | 81 | empty |
| 4 | 1017 | 0.82 | 0.83 | 101 | empty |
| 5 | 919 | 0.78 | 0.81 | 108 | empty |
Interfaces
9 interfaces between chains.
- B–D · 3228 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 3105 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2622 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1869 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1742 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6YLE · Rix1-Rea1 pre-60S particle - Rix1-subcomplex, body 3 (rigid body refinement) · the same entry in another collection · chain K against K, TM-score 1.00
- P38883 · AlphaFold monomer V2.0 prediction for pre-rRNA-processing protein RIX1 (P38883) · a predicted model of the same protein · chain C against A, TM-score 0.97
- P53877 · AlphaFold monomer V2.0 prediction for pre-rRNA-processing protein IPI3 (P53877) · a predicted model of the same protein · chain B against A, TM-score 0.92
- A6ZSZ4 · AlphaFold monomer V2.0 prediction for pre-rRNA-processing protein IPI1 (A6ZSZ4) · a predicted model of the same protein · chain K against A, TM-score 0.46
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 P53877
- Every structure of UniProt P38883
- Every structure of UniProt A6ZSZ4
- Elsewhere: RCSB PDB 6YLE · PDBe 6YLE · UniProt P53877 · UniProt P38883 · UniProt A6ZSZ4
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