Research workbench
Crystal structure of the pabp-binding site of EIF4G in complex with RRM1-2 of pabp and POLY(A)
Analyse Crystal structure of the pabp-binding site of EIF4G in complex with RRM1-2 of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F02
- Type
- protein + RNA
- Length
- 407 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyadenylate-binding protein 1; RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')…
- UniProt
- P11940, Q04637
- Pockets
- 7 · best druggability 0.42
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyadenylate-binding protein 1 | protein | 175 | 33% helix, 35% strand | P11940 |
| B, E | RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') | rna | 9 | — | — |
| C, F | Eukaryotic translation initiation factor 4 gamma 1 | protein | 20 | 40% helix, 25% strand | Q04637 |
| D | Polyadenylate-binding protein 1 | protein | 174 | 31% helix, 36% strand | P11940 |
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.42 | 0.78 | 22 | empty |
| 2 | 70 | 0.38 | 0.78 | 22 | empty |
| 3 | 68 | 0.37 | 0.78 | 24 | empty |
| 4 | 85 | 0.35 | 0.75 | 18 | empty |
| 5 | 87 | 0.33 | 0.74 | 14 | empty |
Interfaces
8 interfaces between chains.
- D–E · 1364 Ų buried · 32 hydrogen bonds · protein-nucleic
- A–B · 1361 Ų buried · 35 hydrogen bonds · protein-nucleic
- D–F · 599 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 553 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 322 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4F02 · Crystal structure of the PABP-binding site of eIF4G in complex with RRM1-2 of PABP and… · the same entry in another collection · chain F against F, TM-score 1.00
- P11940 · AlphaFold monomer V2.0 prediction for polyadenylate-binding protein 1 (P11940) · a predicted model of the same protein · chain D against A, TM-score 0.97
- Q04637 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 4 gamma 1… · a predicted model of the same protein · chain C against A, TM-score 0.63
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 P11940
- Every structure of UniProt Q04637
- Elsewhere: RCSB PDB 4F02 · PDBe 4F02 · UniProt P11940 · UniProt Q04637
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