MolNFT v1 · #191054 · protein + RNA
Cryo-EM structure of AIF1A:AIF5B:MET-trnaimet complex from a pyrococcus abyssi 30S initiation complex
7ZKI: “Cryo-EM structure of AIF1A:AIF5B:MET-trnaimet complex from a pyrococcus abyssi 30S initiation complex”. Electron microscopy, 3 ligands (MET, GNP, MG), 15 pockets (best druggability 0.68). MolNFT v1 #191054 on GenesisL1: 3D…
- PDB
- 7ZKI
- Type
- protein + RNA
- Length
- 764 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Met-trnaimet; Translation initiation factor 1A; Translation initiation factor 5B
- UniProt
- Q9V138, Q9UZK7
- Ligands
- MET, GNP, MG
- Pockets
- 15 · best druggability 0.68
Structure
electron microscopy · 3 distinct chains · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 4 | Met-trnaimet | rna | 77 | — | — |
| 6 | Translation initiation factor 1A | protein | 92 | 21% helix, 34% strand | Q9V138 |
| 7 | Translation initiation factor 5B | protein | 595 | 33% helix, 26% strand | Q9UZK7 |
Ligands and binding sites
- MET · Methionine · ligand · chains 4, 7
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains 7
- MG · Magnesium ion · metal · chains 7
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.68 | 0.91 | 28 | empty |
| 2 | 188 | 0.65 | 0.84 | 24 | empty |
| 3 | 636 | 0.64 | 0.75 | 25 | empty |
| 4 | 177 | 0.58 | 0.81 | 27 | empty |
| 5 | 229 | 0.57 | 0.79 | 28 | empty |
Interfaces
2 interfaces between chains.
- 4–7 · 665 Ų buried · 12 hydrogen bonds · protein-nucleic
- 6–7 · 236 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified, 2 covalent (nucleotide modification, covalent ligand).
Compared structures
- 7ZKI · Cryo-EM structure of aIF1A:aIF5B:Met-tRNAiMet complex from a Pyrococcus abyssi 30S… · the same entry in another collection · chain 4 against 4, TM-score 1.00
- Q9V138 · AlphaFold monomer V2.0 prediction for translation initiation factor 1A (Q9V138) · a predicted model of the same protein · chain 6 against A, TM-score 0.97
- Q9UZK7 · AlphaFold monomer V2.0 prediction for probable translation initiation factor if-2 (Q9UZK7) · a predicted model of the same protein · chain 7 against A, TM-score 0.68
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 Q9V138
- Every structure of UniProt Q9UZK7
- Elsewhere: RCSB PDB 7ZKI · PDBe 7ZKI · UniProt Q9V138 · UniProt Q9UZK7
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