MolNFT v1 · #139232 · protein
Crystal structure of the cytosolic domain of the MG2+ channel mgte in complex with ATP
5X9G · Magnesium transporter mgte: “Crystal structure of the cytosolic domain of the MG2+ channel mgte in complex with ATP”. X-ray diffraction, 2 ligands (ATP, MG), 13 pockets (best druggability 0.79). MolNFT v1 #139232 on GenesisL1: 3D…
- PDB
- 5X9G
- Type
- protein
- Length
- 991 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Magnesium transporter mgte
- UniProt
- Q5SMG8
- Ligands
- ATP, MG
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Magnesium transporter mgte | protein | 248 | 57% helix, 16% strand | Q5SMG8 |
| C | Magnesium transporter mgte | protein | 247 | 56% helix, 14% strand | Q5SMG8 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.79 | 0.80 | 85 | empty |
| 2 | 784 | 0.77 | 0.81 | 76 | empty |
| 3 | 719 | 0.68 | 0.76 | 88 | empty |
| 4 | 241 | 0.49 | 0.75 | 28 | MG |
| 5 | 157 | 0.45 | 0.76 | 23 | empty |
Interfaces
4 interfaces between chains.
- A–D · 930 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 911 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 593 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 585 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5X9G · Crystal structure of the cytosolic domain of the Mg2+ channel MgtE in complex with ATP · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SMG8 · AlphaFold monomer V2.0 prediction for magnesium transporter mgte (Q5SMG8) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q5SMG8
- Elsewhere: RCSB PDB 5X9G · PDBe 5X9G · UniProt Q5SMG8
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