Research workbench
Crystal structure of WD40 repeat domains of GEMIN5 in complex with 13- nt U4 snrna fragment
Analyse Crystal structure of WD40 repeat domains of GEMIN5 in complex with 13- nt U4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H1K
- Type
- protein + RNA
- Length
- 1,389 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gem-associated protein 5; U4 snrna (5'-R(*GP*CP*AP*AP*UP*UP*UP*UP*UP*GP*AP*CP*A)-3')
- UniProt
- Q8TEQ6
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gem-associated protein 5 | protein | 674 | 6% helix, 47% strand | Q8TEQ6 |
| B | Gem-associated protein 5 | protein | 690 | 5% helix, 45% strand | Q8TEQ6 |
| C | U4 snrna (5'-R(*GP*CP*AP*AP*UP*UP*UP*UP*UP*GP*AP*CP*A)-3') | rna | 13 | — | — |
| D | U4 snrna (5'-R(*GP*CP*AP*AP*UP*UP*UP*UP*UP*GP*AP*CP*A)-3') | rna | 12 | — | — |
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 703 | 0.83 | 0.87 | 57 | empty |
| 2 | 706 | 0.83 | 0.87 | 64 | empty |
| 3 | 518 | 0.76 | 0.84 | 45 | empty |
| 4 | 513 | 0.75 | 0.83 | 50 | empty |
| 5 | 614 | 0.68 | 0.77 | 53 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1164 Ų buried · 25 hydrogen bonds · protein-nucleic
- B–D · 1125 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–B · 426 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 181 Ų buried · 9 hydrogen bonds · nucleic-nucleic
- A–D · 102 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 5H1K · Crystal structure of WD40 repeat domains of Gemin5 in complex with 13-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 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 Q8TEQ6
- Elsewhere: RCSB PDB 5H1K · PDBe 5H1K · UniProt Q8TEQ6
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