MolNFT v1 · #99340 · protein
Gamma subunit of the translation initiation factor 2 from sulfolobus solfataricus complexed with GDP
4M0L · Translation initiation factor 2 subunit gamma: “Gamma subunit of the translation initiation factor 2 from sulfolobus solfataricus complexed with GDP”. X-ray diffraction, 3 ligands (GDP, MG, PO4), 20 pockets (best druggability 0.83).…
- PDB
- 4M0L
- Type
- protein
- Length
- 2,438 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Translation initiation factor 2 subunit gamma
- UniProt
- Q980A5
- Ligands
- GDP, MG, PO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 16% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Translation initiation factor 2 subunit gamma | protein | 412 | 16% helix, 38% strand | Q980A5 |
| B | Translation initiation factor 2 subunit gamma | protein | 396 | 18% helix, 38% strand | Q980A5 |
| C | Translation initiation factor 2 subunit gamma | protein | 406 | 16% helix, 37% strand | Q980A5 |
| D, E | Translation initiation factor 2 subunit gamma | protein | 405 | 17% helix, 37% strand | Q980A5 |
| F | Translation initiation factor 2 subunit gamma | protein | 414 | 14% helix, 37% strand | Q980A5 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 6 copies · chains A, C, B, E, D, F
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.83 | 0.86 | 70 | empty |
| 2 | 930 | 0.82 | 0.84 | 76 | empty |
| 3 | 979 | 0.81 | 0.83 | 63 | empty |
| 4 | 790 | 0.81 | 0.84 | 70 | empty |
| 5 | 377 | 0.73 | 0.84 | 50 | empty |
Interfaces
9 interfaces between chains.
- A–D · 1109 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 964 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 759 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 744 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 493 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 4M0L · Gamma subunit of the translation initiation factor 2 from Sulfolobus solfataricus… · the same entry in another collection · chain F against F, TM-score 1.00
- Q980A5 · AlphaFold monomer V2.0 prediction for translation initiation factor 2 subunit gamma… · a predicted model of the same protein · chain B against A, TM-score 0.94
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 4M0L · PDBe 4M0L · UniProt Q980A5
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