MolNFT v1 · #182060 · protein
X-ray structure of the L136 aminotransferase from acanthamoeba polyphaga mimivirus in the presence of tdp and pmp
7MFO: “X-ray structure of the L136 aminotransferase from acanthamoeba polyphaga mimivirus in the presence of tdp and…”. X-ray diffraction, 4 ligands (PMP, TYD, PO4), 20 pockets (best druggability 0.85). MolNFT v1 #182060 on GenesisL1: 3D…
- PDB
- 7MFO
- Type
- protein
- Length
- 3,508 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L136 aminotransferase
- UniProt
- Q5UPL1
- Ligands
- PMP, TYD, PO4, CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L136 aminotransferase | protein | 348 | 42% helix, 16% strand | Q5UPL1 |
| B, F, I | L136 aminotransferase | protein | 350 | 42% helix, 17% strand | Q5UPL1 |
| C, G | L136 aminotransferase | protein | 352 | 42% helix, 16% strand | Q5UPL1 |
| D, H, J | L136 aminotransferase | protein | 351 | 42% helix, 16% strand | Q5UPL1 |
| E | L136 aminotransferase | protein | 353 | 42% helix, 16% strand | Q5UPL1 |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- TYD · Thymidine-5'-diphosphate · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- PO4 · Phosphate ion · ion · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, E, F, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 930 | 0.85 | 0.86 | 117 | PMP |
| 2 | 1146 | 0.85 | 0.86 | 118 | PMP, TYD |
| 3 | 1093 | 0.84 | 0.85 | 108 | TYD, PMP |
| 4 | 550 | 0.76 | 0.83 | 56 | PMP, TYD |
| 5 | 588 | 0.74 | 0.81 | 71 | TYD, PMP |
Interfaces
20 interfaces between chains.
- A–B · 2341 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2308 Ų buried · 41 hydrogen bonds · protein-protein
- E–F · 2300 Ų buried · 44 hydrogen bonds · protein-protein
- G–H · 2263 Ų buried · 43 hydrogen bonds · protein-protein
- I–J · 2245 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 7MFO · X-ray structure of the L136 Aminotransferase from Acanthamoeba polyphaga mimivirus in the… · the same entry in another collection · chain A against A, 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 Q5UPL1
- Elsewhere: RCSB PDB 7MFO · PDBe 7MFO · UniProt Q5UPL1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.