MolNFT v1 · #126353 · protein + RNA
Crystal structure of the cytoplasmic complex with SHE2P, SHE3P, and the ASH1 mRNA E3-localization element
5M0J · SWI5-dependent ho expression protein 2,SWI5-dependent ho…: “Crystal structure of the cytoplasmic complex with SHE2P, SHE3P, and the ASH1 mRNA E3-localization element”. X-ray diffraction, 1 ligand (MG), 16 pockets (best druggability…
- PDB
- 5M0J
- Type
- protein + RNA
- Length
- 1,064 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SWI5-dependent ho expression protein 2,SWI5-dependent ho expression protein 3; ASH1 E3…
- UniProt
- B3LQW9, B3LN26
- Ligands
- MG
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · 9 distinct chains · 71% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | SWI5-dependent ho expression protein 2,SWI5-dependent ho expression protein 3 | protein | 232 | 75% helix, 1% strand | B3LQW9, B3LN26 |
| C | SWI5-dependent ho expression protein 2,SWI5-dependent ho expression protein 3 | protein | 240 | 73% helix, 2% strand | B3LQW9, B3LN26 |
| B | SWI5-dependent ho expression protein 2,SWI5-dependent ho expression protein 3 | protein | 234 | 76% helix, 2% strand | B3LQW9, B3LN26 |
| A | SWI5-dependent ho expression protein 2,SWI5-dependent ho expression protein 3 | protein | 223 | 81% helix, 1% strand | B3LQW9, B3LN26 |
| J | SWI5-dependent ho expression protein 2,SWI5-dependent ho expression protein 3 | protein | 21 | 19% helix, 5% strand | B3LQW9, B3LN26 |
| G | SWI5-dependent ho expression protein 2,SWI5-dependent ho expression protein 3 | protein | 16 | 25% helix, 0% strand | B3LQW9, B3LN26 |
| H | SWI5-dependent ho expression protein 2,SWI5-dependent ho expression protein 3 | protein | 22 | 14% helix, 9% strand | B3LQW9, B3LN26 |
| I | SWI5-dependent ho expression protein 2,SWI5-dependent ho expression protein 3 | protein | 20 | 0% helix, 10% strand | B3LQW9, B3LN26 |
| E, F | ASH1 E3 (28 nt-loop) | rna | 28 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains D, C, B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1053 | 0.80 | 0.82 | 86 | empty |
| 2 | 450 | 0.71 | 0.81 | 58 | empty |
| 3 | 382 | 0.71 | 0.82 | 52 | empty |
| 4 | 300 | 0.66 | 0.83 | 28 | empty |
| 5 | 281 | 0.66 | 0.83 | 25 | empty |
Interfaces
23 interfaces between chains.
- B–A · 2014 Ų buried · 32 hydrogen bonds · protein-protein
- D–C · 1981 Ų buried · 32 hydrogen bonds · protein-protein
- C–I · 1170 Ų buried · 14 hydrogen bonds · protein-protein
- D–J · 1110 Ų buried · 10 hydrogen bonds · protein-protein
- B–H · 996 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5M0J · Crystal structure of the cytoplasmic complex with She2p, She3p, and the ASH1 mRNA… · the same entry in another collection · chain F against F, 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 B3LN26
- Elsewhere: RCSB PDB 5M0J · PDBe 5M0J · UniProt B3LQW9 · UniProt B3LN26
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