Research workbench
Crystal structure of WD40 repeat domains of GEMIN5 in complex with 7- nt U4 snrna fragment
Analyse Crystal structure of WD40 repeat domains of GEMIN5 in complex with 7- nt U4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H1L
- Type
- protein + RNA
- Length
- 689 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gem-associated protein 5; U4 snrna (5'-R(*AP*UP*UP*UP*UP*UP*G)-3')
- UniProt
- Q8TEQ6
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gem-associated protein 5 | protein | 682 | 5% helix, 46% strand | Q8TEQ6 |
| B | U4 snrna (5'-R(*AP*UP*UP*UP*UP*UP*G)-3') | rna | 7 | — | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 856 | 0.80 | 0.82 | 57 | empty |
| 2 | 510 | 0.77 | 0.84 | 52 | empty |
| 3 | 470 | 0.65 | 0.78 | 50 | empty |
| 4 | 341 | 0.59 | 0.77 | 64 | GOL |
| 5 | 99 | 0.39 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 918 Ų buried · 23 hydrogen bonds · protein-nucleic
Compared structures
- 5H1L · Crystal structure of WD40 repeat domains of Gemin5 in complex with 7-nt U4 snRNA fragment · the same entry in another collection · chain A against A, TM-score 1.00
- Q8TEQ6 · AlphaFold monomer V2.0 prediction for gem-associated protein 5 (Q8TEQ6) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q8TEQ6
- Elsewhere: RCSB PDB 5H1L · PDBe 5H1L · UniProt Q8TEQ6
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