Research workbench
Crystal structure of the MG2+ channel mgte in complex with ATP
Analyse Crystal structure of the MG2+ channel mgte in complex with ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X9H
- Type
- protein
- Length
- 853 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Magnesium transporter mgte
- UniProt
- Q5SMG8
- Ligands
- ATP, MG
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Magnesium transporter mgte | protein | 427 | 67% helix, 7% strand | Q5SMG8 |
| B | Magnesium transporter mgte | protein | 426 | 68% helix, 9% strand | Q5SMG8 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 13 copies · 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 | 875 | 0.81 | 0.84 | 105 | MG |
| 2 | 271 | 0.68 | 0.84 | 37 | MG |
| 3 | 51 | 0.67 | 0.97 | 21 | MG |
| 4 | 58 | 0.51 | 0.87 | 15 | empty |
| 5 | 65 | 0.47 | 0.83 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 4967 Ų buried · 48 hydrogen bonds · protein-protein
Compared structures
- 5X9H · Crystal structure 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 0.97
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 5X9H · PDBe 5X9H · UniProt Q5SMG8
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