Research workbench
Structure of the ternary initiation complex AIF2:GDPNP:METHIONYLATED initiator tRNA
Analyse Structure of the ternary initiation complex AIF2:GDPNP:METHIONYLATED initiator… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V11
- Type
- protein + RNA
- Length
- 751 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Translation initiation factor 2 subunit gamma; Translation initiation factor 2 subunit…
- UniProt
- Q980A5, Q97Z79, Q97W59
- Ligands
- GNP, MET, MG
- Pockets
- 12 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Translation initiation factor 2 subunit gamma | protein | 404 | 17% helix, 35% strand | Q980A5 |
| B | Translation initiation factor 2 subunit alpha | protein | 254 | 37% helix, 24% strand | Q97Z79 |
| C | Translation initiation factor 2 subunit beta | protein | 17 | 65% helix, 0% strand | Q97W59 |
| D | Initiator tRNA | rna | 76 | — | — |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
- MET · Methionine · ligand · chains A, D
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 639 | 0.65 | 0.76 | 29 | empty |
| 2 | 339 | 0.61 | 0.78 | 37 | empty |
| 3 | 180 | 0.58 | 0.82 | 36 | MET |
| 4 | 258 | 0.52 | 0.76 | 16 | empty |
| 5 | 146 | 0.47 | 0.77 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–B · 916 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 789 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 726 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–D · 721 Ų buried · 10 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 5 modified, 1 covalent (nucleotide modification, covalent ligand).
Compared structures
- 3V11 · Structure of the ternary initiation complex AIF2:GDPNP:methionylated initiator TRNA · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.98
- Q97Z79 · AlphaFold monomer V2.0 prediction for translation initiation factor 2 subunit alpha… · a predicted model of the same protein · chain B against A, TM-score 0.81
- Q97W59 · AlphaFold monomer V2.0 prediction for translation initiation factor 2 subunit beta… · a predicted model of the same protein · chain C against A, TM-score 0.61
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
- Every structure of UniProt Q97Z79
- Every structure of UniProt Q97W59
- Elsewhere: RCSB PDB 3V11 · PDBe 3V11 · UniProt Q980A5 · UniProt Q97Z79 · UniProt Q97W59
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