MolNFT v1 · #150865 · protein
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.
6H6K · Translation initiation factor 2 subunit gamma: “The structure of the fkr mutant of the archaeal translation initiation factor 2 gamma subunit in complex with…”. X-ray diffraction, 2 ligands (GCP, NA), 20 pockets (best druggability…
- 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.