Research workbench
Pandda analysis group deposition -- crystal structure of human ALAS2A in complex with Z2856434899
Analyse Pandda analysis group deposition -- crystal structure of human ALAS2A in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5QQY
- Type
- protein
- Length
- 857 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-aminolevulinate synthase, erythroid-specific, mitochondrial
- EC
- 2.3.1.37
- UniProt
- P22557
- Ligands
- PLP, NUG
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5-aminolevulinate synthase, erythroid-specific, mitochondrial (EC 2.3.1.37) | protein | 428 | 44% helix, 15% strand | P22557 |
| A | 5-aminolevulinate synthase, erythroid-specific, mitochondrial (EC 2.3.1.37) | protein | 429 | 44% helix, 15% strand | P22557 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains B, A
- NUG · 1-[(2,5-dihydrothiophen-3-yl)methyl]piperidin-4-ol · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.82 | 0.94 | 56 | PLP |
| 2 | 223 | 0.81 | 0.95 | 49 | PLP |
| 3 | 140 | 0.51 | 0.80 | 18 | NUG |
| 4 | 142 | 0.50 | 0.79 | 20 | NUG |
| 5 | 159 | 0.46 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- B–A · 5071 Ų buried · 57 hydrogen bonds · protein-protein
Compared structures
- 5QQY · PanDDA analysis group deposition -- Crystal Structure of human ALAS2A in complex with… · the same entry in another collection · chain B against B, TM-score 1.00
- P22557 · AlphaFold monomer V2.0 prediction for 5-aminolevulinate synthase, erythroid-specific… · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P22557
- Elsewhere: RCSB PDB 5QQY · PDBe 5QQY · UniProt P22557
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