Research workbench
Electron transfer flavoprotein (etf) from paracoccus denitrificans
Analyse Electron transfer flavoprotein (etf) from paracoccus denitrificans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EFP
- Type
- protein
- Length
- 1,106 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (electron transfer flavoprotein)
- UniProt
- P38974, P38975
- Ligands
- FAD, AMP
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Protein (electron transfer flavoprotein) | protein | 307 | 31% helix, 28% strand | P38974 |
| B, D | Protein (electron transfer flavoprotein) | protein | 246 | 27% helix, 32% strand | P38975 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B, C, D
- AMP · Adenosine monophosphate · ligand · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 430 | 0.83 | 0.91 | 59 | AMP |
| 2 | 460 | 0.82 | 0.89 | 59 | AMP |
| 3 | 681 | 0.78 | 0.83 | 96 | empty |
| 4 | 453 | 0.74 | 0.83 | 67 | empty |
| 5 | 80 | 0.70 | 0.95 | 19 | empty |
Interfaces
3 interfaces between chains.
- C–D · 3281 Ų buried · 63 hydrogen bonds · protein-protein
- A–B · 3201 Ų buried · 64 hydrogen bonds · protein-protein
- A–C · 205 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1EFP · Electron transfer flavoprotein (etf) from paracoccus denitrificans · the same entry in another collection · chain D against D, TM-score 1.00
- P38975 · AlphaFold monomer V2.0 prediction for electron transfer flavoprotein subunit beta (P38975) · a predicted model of the same protein · chain D against A, TM-score 0.98
- P38974 · AlphaFold monomer V2.0 prediction for electron transfer flavoprotein subunit alpha… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P38974
- Every structure of UniProt P38975
- Elsewhere: RCSB PDB 1EFP · PDBe 1EFP · UniProt P38974 · UniProt P38975
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