Research workbench
The structure of the fkr mutant of the archaeal translation initiation factor 2 gamma subunit in complex with gdpcp, obtained in the absence of magnesium salts in the crystallization solution.
Analyse The structure of the fkr mutant of the archaeal translation initiation factor 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H6K
- Type
- protein
- Length
- 2,047 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Translation initiation factor 2 subunit gamma
- UniProt
- Q980A5
- Ligands
- GCP, NA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 17% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Translation initiation factor 2 subunit gamma | protein | 413 | 17% helix, 40% strand | Q980A5 |
| B | Translation initiation factor 2 subunit gamma | protein | 407 | 18% helix, 41% strand | Q980A5 |
| C | Translation initiation factor 2 subunit gamma | protein | 413 | 17% helix, 41% strand | Q980A5 |
| D | Translation initiation factor 2 subunit gamma | protein | 409 | 17% helix, 42% strand | Q980A5 |
| E | Translation initiation factor 2 subunit gamma | protein | 405 | 16% helix, 40% strand | Q980A5 |
Ligands and binding sites
- GCP · Phosphomethylphosphonic acid guanylate ester · ligand · 5 copies · chains A, B, C, D, E
- NA · Sodium ion · metal · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 754 | 0.82 | 0.85 | 91 | EDO |
| 2 | 931 | 0.82 | 0.84 | 92 | empty |
| 3 | 770 | 0.79 | 0.82 | 67 | empty |
| 4 | 314 | 0.63 | 0.79 | 35 | empty |
| 5 | 329 | 0.62 | 0.78 | 37 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1153 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 1123 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 799 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 723 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 680 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- Q980A5 · AlphaFold monomer V2.0 prediction for translation initiation factor 2 subunit gamma… · a predicted model of the same protein · chain E against A, TM-score 0.99
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 Q980A5
- Elsewhere: RCSB PDB 6H6K · PDBe 6H6K · UniProt Q980A5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.