Research workbench
Crystal structure of EIF4E from C. melo bound to a cap analog
Analyse Crystal structure of EIF4E from C. melo bound to a cap analog in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ME6
- Type
- protein
- Length
- 696 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic transcription initiation factor 4E
- UniProt
- Q00LS8
- Ligands
- M7G
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eukaryotic transcription initiation factor 4E | protein | 175 | 31% helix, 31% strand | Q00LS8 |
| B | Eukaryotic transcription initiation factor 4E | protein | 173 | 31% helix, 32% strand | Q00LS8 |
| C | Eukaryotic transcription initiation factor 4E | protein | 179 | 26% helix, 31% strand | Q00LS8 |
| D | Eukaryotic transcription initiation factor 4E | protein | 169 | 30% helix, 33% strand | Q00LS8 |
Ligands and binding sites
- M7G · 7N-methyl-8-hydroguanosine-5'-diphosphate · ligand · 2 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 895 | 0.69 | 0.75 | 75 | empty |
| 2 | 516 | 0.62 | 0.75 | 46 | empty |
| 3 | 124 | 0.53 | 0.81 | 13 | empty |
| 4 | 195 | 0.44 | 0.73 | 28 | M7G |
| 5 | 108 | 0.36 | 0.74 | 27 | empty |
Interfaces
6 interfaces between chains.
- B–C · 639 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 428 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 228 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 82 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 35 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5ME6 · Crystal Structure of eiF4E from C. melo bound to a CAP analog · the same entry in another collection · chain A against A, TM-score 1.00
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 Q00LS8
- Elsewhere: RCSB PDB 5ME6 · PDBe 5ME6 · UniProt Q00LS8
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