Research workbench
Crystal structure of mnme from nostoc in complex with GDP, folinic acid and zn
Analyse Crystal structure of mnme from nostoc in complex with GDP, folinic acid and zn in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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