Research workbench
Crystal structure of the nuclear complex with SHE2P and the ASH1 mRNA E3-localization element
Analyse Crystal structure of the nuclear complex with SHE2P and the ASH1 mRNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M0I
- Type
- protein + RNA
- Length
- 1,016 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SWI5-dependent ho expression protein 2; ASH1-E3 element, RNA (28-mer); SWI5-dependent ho…
- UniProt
- B3LQW9, P38272
- Ligands
- MG
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 7 distinct chains · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | SWI5-dependent ho expression protein 2 | protein | 235 | 75% helix, 1% strand | B3LQW9 |
| C | SWI5-dependent ho expression protein 2 | protein | 240 | 73% helix, 1% strand | B3LQW9 |
| B | SWI5-dependent ho expression protein 2 | protein | 238 | 72% helix, 1% strand | B3LQW9 |
| A | SWI5-dependent ho expression protein 2 | protein | 225 | 78% helix, 1% strand | B3LQW9 |
| E, F | ASH1-E3 element, RNA (28-mer) | rna | 28 | — | — |
| H | SWI5-dependent ho expression protein 3 | protein | 8 | 0% helix, 13% strand | P38272 |
| J, I | SWI5-dependent ho expression protein 3 | protein | 7 | 0% helix, 0% strand | P38272 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains D, C, B, A, F
- EDO · 1,2-ethanediol · additive · 11 copies · chains D, C, F, B, A, E
- ACT · Acetate ion · additive · 6 copies · chains D, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1021 | 0.81 | 0.82 | 89 | empty |
| 2 | 576 | 0.75 | 0.82 | 66 | EDO |
| 3 | 432 | 0.74 | 0.84 | 52 | empty |
| 4 | 265 | 0.67 | 0.84 | 27 | empty |
| 5 | 187 | 0.50 | 0.77 | 27 | EDO |
Interfaces
16 interfaces between chains.
- B–A · 2076 Ų buried · 25 hydrogen bonds · protein-protein
- D–C · 2061 Ų buried · 25 hydrogen bonds · protein-protein
- C–F · 869 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–E · 856 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–H · 503 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5M0I · Crystal structure of the nuclear complex with She2p and the ASH1 mRNA E3-localization… · the same entry in another collection · chain I against I, TM-score 1.00
- B3LQW9 · AlphaFold monomer V2.0 prediction for SWI5-dependent ho expression protein 2 (B3LQW9) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 B3LQW9
- Every structure of UniProt P38272
- Elsewhere: RCSB PDB 5M0I · PDBe 5M0I · UniProt B3LQW9 · UniProt P38272
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.