MolNFT v1 · #3762 · protein
Crystal structure of mitochondrial ef-tu in complex with GDP
1D2E · Elongation factor tu (ef-tu): “Crystal structure of mitochondrial ef-tu in complex with GDP”. X-ray diffraction, 2 ligands (GDP, MG), 15 pockets (best druggability 0.75). MolNFT v1 #3762 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1D2E
- Type
- protein
- Length
- 1,588 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongation factor tu (ef-tu)
- UniProt
- P49410
- Ligands
- GDP, MG
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Elongation factor tu (ef-tu) | protein | 397 | 23% helix, 37% strand | P49410 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1101 | 0.75 | 0.78 | 97 | empty |
| 2 | 462 | 0.70 | 0.81 | 51 | empty |
| 3 | 496 | 0.68 | 0.79 | 37 | empty |
| 4 | 278 | 0.62 | 0.80 | 35 | empty |
| 5 | 333 | 0.61 | 0.78 | 54 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1037 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 601 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 304 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 11 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1D2E · Crystal structure of mitochondrial ef-tu in complex with GDP · the same entry in another collection · chain D against D, TM-score 1.00
- P49410 · AlphaFold monomer V2.0 prediction for elongation factor tu, mitochondrial (P49410) · a predicted model of the same protein · chain B against A, TM-score 0.57
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 P49410
- Elsewhere: RCSB PDB 1D2E · PDBe 1D2E · UniProt P49410
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