MolNFT v1 · #117784 · protein + RNA
Yth domain-containing protein MMI1 and RNA complex
5EIM: “Yth domain-containing protein MMI1 and RNA complex”. X-ray diffraction, 4 pockets (best druggability 0.72). MolNFT v1 #117784 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5EIM
- Type
- protein + RNA
- Length
- 334 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yth domain-containing protein MMI1; RNA (5'-R(*AP*UP*UP*AP*AP*AP*CP*A)-3')
- UniProt
- O74958
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yth domain-containing protein MMI1 | protein | 157 | 31% helix, 34% strand | O74958 |
| B | Yth domain-containing protein MMI1 | protein | 161 | 29% helix, 34% strand | O74958 |
| C, D | RNA (5'-R(*AP*UP*UP*AP*AP*AP*CP*A)-3') | rna | 8 | — | — |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 807 | 0.72 | 0.78 | 58 | empty |
| 2 | 63 | 0.43 | 0.82 | 20 | empty |
| 3 | 54 | 0.36 | 0.79 | 17 | empty |
| 4 | 50 | 0.26 | 0.74 | 12 | empty |
Interfaces
5 interfaces between chains.
- A–C · 789 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–D · 711 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–C · 214 Ų buried · 3 hydrogen bonds · protein-nucleic
- A–B · 211 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 17 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Compared structures
- 5EIM · YTH domain-containing protein mmi1 and RNA complex · the same entry in another collection · chain A against A, TM-score 1.00
- O74958 · AlphaFold monomer V2.0 prediction for RNA binding exosome specificity factor MMI1 (O74958) · a predicted model of the same protein · chain A 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 O74958
- Elsewhere: RCSB PDB 5EIM · PDBe 5EIM · UniProt O74958
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