MolNFT v1 · #132224 · protein
Pandda analysis group deposition -- crystal structure of human ALAS2A in complex with Z1348371854
5QQU · 5-aminolevulinate synthase, erythroid-specific…: “Pandda analysis group deposition -- crystal structure of human ALAS2A in complex with Z1348371854”. X-ray diffraction, 2 ligands (NTG, PLP), 10 pockets (best druggability 0.82).…
- PDB
- 5QQU
- 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
- NTG, PLP
- Pockets
- 10 · 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
- NTG · 5-(1,4-oxazepan-4-yl)pyridine-2-carbonitrile · ligand · 3 copies · chains B, A
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 247 | 0.82 | 0.95 | 57 | PLP |
| 2 | 229 | 0.81 | 0.94 | 50 | PLP |
| 3 | 139 | 0.51 | 0.79 | 18 | empty |
| 4 | 139 | 0.50 | 0.79 | 18 | empty |
| 5 | 151 | 0.46 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- B–A · 5073 Ų buried · 59 hydrogen bonds · protein-protein
Compared structures
- 5QQU · 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 5QQU · PDBe 5QQU · UniProt P22557
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