Research workbench
Crystal structure of ef-pyl in complex with GDP
Analyse Crystal structure of ef-pyl in complex with GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WNC
- Type
- protein
- Length
- 361 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein translation elongation factor 1A
- UniProt
- Q8PXB3
- Ligands
- GDP, MG
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein translation elongation factor 1A | protein | 361 | 20% helix, 42% strand | Q8PXB3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 378 | 0.67 | 0.80 | 29 | empty |
| 2 | 125 | 0.49 | 0.79 | 22 | empty |
| 3 | 89 | 0.43 | 0.79 | 27 | empty |
| 4 | 50 | 0.25 | 0.73 | 15 | empty |
Modifications
Observed in the structure: 5 modified (engineered).
Compared structures
- 3WNC · Crystal structure of EF-Pyl in complex with GDP · 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 Q8PXB3
- Elsewhere: RCSB PDB 3WNC · PDBe 3WNC · UniProt Q8PXB3
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