MolNFT v1 · #37999 · protein
Structure of the mnme G-domain in complex with GDP*ALF4-, MG2+ and K+
2GJ8 · TRNA modification GTPase trme: “Structure of the mnme G-domain in complex with GDP*ALF4-, MG2+ and K+”. X-ray diffraction, 5 ligands (ALF, GDP, MG), 7 pockets (best druggability 0.61). MolNFT v1 #37999 on GenesisL1: 3D structure…
- PDB
- 2GJ8
- Type
- protein
- Length
- 654 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA modification GTPase trme
- UniProt
- P25522
- Ligands
- ALF, GDP, MG, K, SE
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | TRNA modification GTPase trme | protein | 161 | 30% helix, 27% strand | P25522 |
| B | TRNA modification GTPase trme | protein | 160 | 31% helix, 26% strand | P25522 |
| D | TRNA modification GTPase trme | protein | 172 | 30% helix, 23% strand | P25522 |
Ligands and binding sites
- ALF · Tetrafluoroaluminate ion · ligand · 4 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- SE · Selenium atom · ion · 3 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.61 | 0.87 | 26 | ALF, MG, K, GDP |
| 2 | 101 | 0.59 | 0.87 | 28 | ALF, MG, K, GDP |
| 3 | 207 | 0.59 | 0.81 | 31 | ALF, MG, K, GDP |
| 4 | 196 | 0.57 | 0.80 | 39 | ALF, MG, K, GDP |
| 5 | 207 | 0.56 | 0.79 | 31 | empty |
Interfaces
4 interfaces between chains.
- C–D · 868 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 842 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 217 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 200 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 2GJ8 · Structure of the MnmE G-domain in complex with GDP*AlF4-, Mg2+ and K+ · the same entry in another collection · chain A against A, TM-score 1.00
- P25522 · AlphaFold monomer V2.0 prediction for tRNA modification GTPase mnme (P25522) · a predicted model of the same protein · chain A against A, TM-score 0.82
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 P25522
- Elsewhere: RCSB PDB 2GJ8 · PDBe 2GJ8 · UniProt P25522
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