Research workbench
Crystal structure of yjeq from thermotoga maritima
Analyse Crystal structure of yjeq from thermotoga maritima in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1U0L
- Type
- protein
- Length
- 834 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable GTPase engc
- EC
- 3.6.1.-
- UniProt
- Q9X242
- Ligands
- GDP, ZN
- Pockets
- 7 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Probable GTPase engc (EC 3.6.1.-) | protein | 278 | 28% helix, 22% strand | Q9X242 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.62 | 0.81 | 39 | empty |
| 2 | 190 | 0.54 | 0.78 | 34 | empty |
| 3 | 114 | 0.45 | 0.78 | 27 | empty |
| 4 | 79 | 0.43 | 0.80 | 17 | empty |
| 5 | 84 | 0.42 | 0.78 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1019 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 928 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 907 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1U0L · Crystal structure of YjeQ from Thermotoga maritima · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X242 · AlphaFold monomer V2.0 prediction for small ribosomal subunit biogenesis GTPase rsga… · 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 Q9X242
- Elsewhere: RCSB PDB 1U0L · PDBe 1U0L · UniProt Q9X242
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