MolNFT v1 · #141582 · protein + RNA
Crystal structure of the human EIF4A1-ATP analog-roca-polypurine RNA complex
5ZC9 · Eukaryotic initiation factor 4A-I: “Crystal structure of the human EIF4A1-ATP analog-roca-polypurine RNA complex”. X-ray diffraction, 3 ligands (ANP, RCG, MG), 3 pockets (best druggability 0.65). MolNFT v1 #141582 on GenesisL1: 3D…
- PDB
- 5ZC9
- Type
- protein + RNA
- Length
- 388 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic initiation factor 4A-I; RNA (5'-R(*AP*GP*AP*GP*AP*GP*AP*GP*AP*G)-3')
- EC
- 3.6.4.13
- UniProt
- P60842
- Ligands
- ANP, RCG, MG
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eukaryotic initiation factor 4A-I (EC 3.6.4.13) | protein | 378 | 44% helix, 17% strand | P60842 |
| B | RNA (5'-R(*AP*GP*AP*GP*AP*GP*AP*GP*AP*G)-3') | rna | 10 | — | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- RCG · (1R,2R,3S,3aR,8bS)-6,8-dimethoxy-3a-(4-methoxyphenyl)-N,N-dimethyl-1,8b-bis(oxidanyl)-3-phenyl-2,3-dihydro-1H-cyclopenta[b][1]benzofuran-2-carboxamide · ligand · chains A, B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.65 | 0.81 | 42 | ANP, MG |
| 2 | 188 | 0.57 | 0.81 | 28 | empty |
| 3 | 58 | 0.35 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 886 Ų buried · 40 hydrogen bonds · protein-nucleic
Compared structures
- 5ZC9 · Crystal structure of the human eIF4A1-ATP analog-RocA-polypurine RNA complex · the same entry in another collection · chain A against A, TM-score 1.00
- P60842 · AlphaFold monomer V2.0 prediction for eukaryotic initiation factor 4A-I (P60842) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P60842
- Elsewhere: RCSB PDB 5ZC9 · PDBe 5ZC9 · UniProt P60842
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