MolNFT v1 · #120476 · protein
Crystal structure of WD40 repeat domains of GEMIN5 in complex with M7G
5H1M · Gem-associated protein 5: “Crystal structure of WD40 repeat domains of GEMIN5 in complex with M7G”. X-ray diffraction, 1 ligand (M7G), 8 pockets (best druggability 0.81). MolNFT v1 #120476 on GenesisL1: 3D structure, binding sites…
- 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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