MolNFT v1 · #148623 · protein
Crystal structure of the EIF4E-EAP1P complex from saccharomyces cerevisiae in the cap-bound state
6FC1 · Eukaryotic translation initiation factor 4E: “Crystal structure of the EIF4E-EAP1P complex from saccharomyces cerevisiae in the cap-bound state”. X-ray diffraction, 1 ligand (MGP), 6 pockets (best druggability 0.53). MolNFT v1…
- PDB
- 6FC1
- Type
- protein
- Length
- 479 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic translation initiation factor 4E; Protein EAP1
- UniProt
- P07260, P36041
- Ligands
- MGP
- Pockets
- 6 · best druggability 0.53
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eukaryotic translation initiation factor 4E | protein | 181 | 23% helix, 30% strand | P07260 |
| B | Protein EAP1 | protein | 64 | 39% helix, 0% strand | P36041 |
| C | Eukaryotic translation initiation factor 4E | protein | 181 | 23% helix, 29% strand | P07260 |
| D | Protein EAP1 | protein | 53 | 42% helix, 0% strand | P36041 |
Ligands and binding sites
- MGP · 7-methyl-guanosine-5'-triphosphate · ligand · 2 copies · chains A, C
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.53 | 0.75 | 33 | GOL |
| 2 | 110 | 0.41 | 0.76 | 25 | MGP |
| 3 | 54 | 0.38 | 0.80 | 13 | empty |
| 4 | 89 | 0.36 | 0.75 | 21 | MGP |
| 5 | 56 | 0.30 | 0.76 | 10 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2266 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2172 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 279 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 200 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 95 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6FC1 · Crystal structure of the eIF4E-Eap1p complex from Saccharomyces cerevisiae in the… · the same entry in another collection · chain D against D, TM-score 1.00
- P07260 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 4E (P07260) · a predicted model of the same protein · chain C against A, TM-score 0.94
- P36041 · AlphaFold monomer V2.0 prediction for protein EAP1 (P36041) · a predicted model of the same protein · chain D against A, TM-score 0.49
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 P07260
- Every structure of UniProt P36041
- Elsewhere: RCSB PDB 6FC1 · PDBe 6FC1 · UniProt P07260 · UniProt P36041
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