MolNFT v1 · #135393 · protein
Structure of asymmetric APO/HOLO alas dimer from S. cerevisiae
5TXT · 5-aminolevulinate synthase, mitochondrial: “Structure of asymmetric APO/HOLO alas dimer from S. cerevisiae”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.81). MolNFT v1 #135393 on GenesisL1: 3D structure…
- PDB
- 5TXT
- Type
- protein
- Length
- 2,714 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-aminolevulinate synthase, mitochondrial
- EC
- 2.3.1.37
- UniProt
- P09950
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | 5-aminolevulinate synthase, mitochondrial (EC 2.3.1.37) | protein | 448 | 43% helix, 13% strand | P09950 |
| B, F | 5-aminolevulinate synthase, mitochondrial (EC 2.3.1.37) | protein | 460 | 44% helix, 14% strand | P09950 |
| D | 5-aminolevulinate synthase, mitochondrial (EC 2.3.1.37) | protein | 441 | 44% helix, 13% strand | P09950 |
| C | 5-aminolevulinate synthase, mitochondrial (EC 2.3.1.37) | protein | 457 | 44% helix, 14% strand | P09950 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains D
- PE3 · 3,6,9,12,15,18,21,24,27,30,33,36,39-tridecaoxahentetracontane-1,41-diol · additive · 7 copies · chains B, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 872 | 0.81 | 0.84 | 99 | empty |
| 2 | 933 | 0.79 | 0.81 | 109 | empty |
| 3 | 1080 | 0.79 | 0.81 | 114 | empty |
| 4 | 1100 | 0.78 | 0.80 | 126 | empty |
| 5 | 1005 | 0.78 | 0.80 | 103 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3706 Ų buried · 51 hydrogen bonds · protein-protein
- D–C · 3693 Ų buried · 54 hydrogen bonds · protein-protein
- E–F · 3641 Ų buried · 55 hydrogen bonds · protein-protein
- A–C · 714 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 638 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (cofactor).
Compared structures
- 5TXT · Structure of asymmetric apo/holo ALAS dimer from S. cerevisiae · the same entry in another collection · chain F against F, TM-score 1.00
- P09950 · AlphaFold monomer V2.0 prediction for 5-aminolevulinate synthase, mitochondrial (P09950) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P09950
- Elsewhere: RCSB PDB 5TXT · PDBe 5TXT · UniProt P09950
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