MolNFT v1 · #186511 · protein
O2-, plp-dependent desaturase PLU4 product-bound enzyme
7RGB · AMINOTRAN_1_2 domain-containing protein: “O2-, plp-dependent desaturase PLU4 product-bound enzyme”. X-ray diffraction, 1 ligand (4VI), 19 pockets (best druggability 0.75). MolNFT v1 #186511 on GenesisL1: 3D structure, binding sites…
- PDB
- 7RGB
- Type
- protein
- Length
- 1,486 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
- 4VI
- Pockets
- 19 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | AMINOTRAN_1_2 domain-containing protein | protein | 372 | 51% helix, 13% strand | A0A0C1MLE8 |
| B, D | AMINOTRAN_1_2 domain-containing protein | protein | 371 | 50% helix, 14% strand | A0A0C1MLE8 |
Ligands and binding sites
- 4VI · (2Z,4E)-5-carbamimidamido-2-iminopent-4-enoic acid · ligand · 2 copies · chains A, B, C, D
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.75 | 0.98 | 22 | empty |
| 2 | 70 | 0.74 | 0.98 | 22 | empty |
| 3 | 188 | 0.65 | 0.85 | 31 | empty |
| 4 | 497 | 0.64 | 0.76 | 61 | EDO, BTB |
| 5 | 268 | 0.63 | 0.81 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2344 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2341 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 268 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 7RGB · O2-, PLP-dependent desaturase Plu4 product-bound enzyme · the same entry in another collection · chain B against B, 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 7RGB · PDBe 7RGB · UniProt A0A0C1MLE8
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