Research workbench
O2-, plp-dependent desaturase PLU4 intermediate-bound enzyme
Analyse O2-, plp-dependent desaturase PLU4 intermediate-bound enzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RF9
- Type
- protein
- Length
- 1,513 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AMINOTRAN_1_2 domain-containing protein
- UniProt
- A0A0C1MLE8
- Ligands
- EJ1, AE3
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | AMINOTRAN_1_2 domain-containing protein | protein | 381 | 51% helix, 13% strand | A0A0C1MLE8 |
| B | AMINOTRAN_1_2 domain-containing protein | protein | 381 | 51% helix, 13% strand | A0A0C1MLE8 |
| C | AMINOTRAN_1_2 domain-containing protein | protein | 376 | 52% helix, 14% strand | A0A0C1MLE8 |
| D | AMINOTRAN_1_2 domain-containing protein | protein | 375 | 51% helix, 14% strand | A0A0C1MLE8 |
Ligands and binding sites
- EJ1 · (2E)-5-carbamimidamido-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}pentanoic acid · ligand · 4 copies · chains A, B, C, D
- AE3 · 2-(2-ethoxyethoxy)ethanol · ligand · chains C
- EDO · 1,2-ethanediol · additive · 19 copies · chains A, B, C, D
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 5 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 5 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.80 | 0.97 | 31 | EJ1 |
| 2 | 137 | 0.80 | 0.97 | 33 | EJ1 |
| 3 | 124 | 0.79 | 0.98 | 30 | EJ1 |
| 4 | 124 | 0.79 | 0.97 | 32 | EJ1 |
| 5 | 76 | 0.74 | 0.98 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2347 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2344 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 397 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7RF9 · O2-, PLP-dependent desaturase Plu4 intermediate-bound enzyme · the same entry in another collection · chain C against C, 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 A0A0C1MLE8
- Elsewhere: RCSB PDB 7RF9 · PDBe 7RF9 · UniProt A0A0C1MLE8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.