Research workbench
Crystal structure of WD40 repeat domains of GEMIN5 in complex with M7G
Analyse Crystal structure of WD40 repeat domains of GEMIN5 in complex with M7G in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H1M
- Type
- protein
- Length
- 674 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gem-associated protein 5
- UniProt
- Q8TEQ6
- Ligands
- M7G
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gem-associated protein 5 | protein | 674 | 5% helix, 47% strand | Q8TEQ6 |
Ligands and binding sites
- M7G · 7N-methyl-8-hydroguanosine-5'-diphosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.81 | 0.82 | 66 | M7G |
| 2 | 484 | 0.74 | 0.83 | 44 | empty |
| 3 | 241 | 0.48 | 0.74 | 29 | empty |
| 4 | 136 | 0.47 | 0.78 | 33 | empty |
| 5 | 82 | 0.37 | 0.76 | 19 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5H1M · Crystal structure of WD40 repeat domains of Gemin5 in complex with M7G · 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 5H1M · PDBe 5H1M · UniProt Q8TEQ6
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