MolNFT v1 · #64815 · protein
Crystal structure of mnme from nostoc in complex with GDP, folinic acid and zn
3GEH · TRNA modification GTPase mnme: “Crystal structure of mnme from nostoc in complex with GDP, folinic acid and zn”. X-ray diffraction, 3 ligands (GDP, FON, ZN), 3 pockets (best druggability 0.46). MolNFT v1 #64815 on GenesisL1: 3D…
- PDB
- 3GEH
- Type
- protein
- Length
- 442 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA modification GTPase mnme
- EC
- 3.6.-.-
- UniProt
- Q8YN91
- Ligands
- GDP, FON, ZN
- Pockets
- 3 · best druggability 0.46
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA modification GTPase mnme (EC 3.6.-.-) | protein | 442 | 42% helix, 17% strand | Q8YN91 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- FON · N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.46 | 0.80 | 29 | empty |
| 2 | 104 | 0.44 | 0.78 | 18 | empty |
| 3 | 72 | 0.42 | 0.80 | 18 | empty |
Compared structures
- 3GEH · Crystal structure of MnmE from Nostoc in complex with GDP, FOLINIC ACID and ZN · the same entry in another collection · chain A against A, TM-score 1.00
- Q8YN91 · AlphaFold monomer V2.0 prediction for tRNA modification GTPase mnme (Q8YN91) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q8YN91
- Elsewhere: RCSB PDB 3GEH · PDBe 3GEH · UniProt Q8YN91
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