Research workbench
Binary structure of human decr solved by semet sad.
Analyse Binary structure of human decr solved by semet sad. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W73
- Type
- protein
- Length
- 1,134 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,4-dienoyl-CoA reductase
- EC
- 1.3.1.34
- UniProt
- Q16698
- Ligands
- NAP
- Pockets
- 14 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2,4-dienoyl-CoA reductase (EC 1.3.1.34) | protein | 288 | 51% helix, 14% strand | Q16698 |
| B | 2,4-dienoyl-CoA reductase (EC 1.3.1.34) | protein | 282 | 51% helix, 14% strand | Q16698 |
| C | 2,4-dienoyl-CoA reductase (EC 1.3.1.34) | protein | 284 | 52% helix, 14% strand | Q16698 |
| D | 2,4-dienoyl-CoA reductase (EC 1.3.1.34) | protein | 280 | 51% helix, 15% strand | Q16698 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 830 | 0.87 | 0.90 | 66 | empty |
| 2 | 723 | 0.71 | 0.77 | 71 | NAP |
| 3 | 518 | 0.66 | 0.77 | 49 | NAP |
| 4 | 413 | 0.63 | 0.77 | 45 | NAP |
| 5 | 385 | 0.62 | 0.77 | 38 | NAP |
Interfaces
6 interfaces between chains.
- C–D · 2372 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2349 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1540 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1529 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1451 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified (engineered).
Compared structures
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 Q16698
- Elsewhere: RCSB PDB 1W73 · PDBe 1W73 · UniProt Q16698
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