MolNFT v1 · #38001 · protein
Structure of the mnme G-domain in complex with GDP*ALF4-, MG2+ and NH4+
2GJA · TRNA modification GTPase trme: “Structure of the mnme G-domain in complex with GDP*ALF4-, MG2+ and NH4+”. X-ray diffraction, 4 ligands (ALF, GDP, MG), 3 pockets (best druggability 0.59). MolNFT v1 #38001 on GenesisL1: 3D structure…
- PDB
- 2GJA
- Type
- protein
- Length
- 329 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA modification GTPase trme
- UniProt
- P25522
- Ligands
- ALF, GDP, MG, NH4
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA modification GTPase trme | protein | 168 | 30% helix, 26% strand | P25522 |
| B | TRNA modification GTPase trme | protein | 161 | 30% helix, 27% strand | P25522 |
Ligands and binding sites
- ALF · Tetrafluoroaluminate ion · ligand · 2 copies · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NH4 · Ammonium ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.59 | 0.86 | 27 | ALF, MG, NH4, GDP |
| 2 | 125 | 0.57 | 0.84 | 27 | ALF, MG, NH4, GDP |
| 3 | 108 | 0.45 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 821 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2GJA · Structure of the MnmE G-domain in complex with GDP*AlF4-, Mg2+ and NH4+ · 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 B 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 2GJA · PDBe 2GJA · UniProt P25522
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