MolNFT v1 · #19876 · protein
Structural basis for the potent antisickling effect of a novel class of 5-membered heterocyclic aldehydic compounds
1QXE · Hemoglobin alpha chain: “Structural basis for the potent antisickling effect of a novel class of 5-membered heterocyclic aldehydic…”. X-ray diffraction, 4 ligands (HEM, FUX, SO4), 6 pockets (best druggability 0.84). MolNFT v1 #19876…
- PDB
- 1QXE
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin alpha chain; Hemoglobin beta chain
- UniProt
- P69905, P68871
- Ligands
- HEM, FUX, SO4, OXY
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin alpha chain | protein | 141 | 79% helix, 0% strand | P69905 |
| B, D | Hemoglobin beta chain | protein | 146 | 78% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- FUX · 5-hydroxymethyl-furfural · ligand · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, D, C
- OXY · Oxygen molecule · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 618 | 0.84 | 0.89 | 92 | SO4 |
| 2 | 209 | 0.74 | 0.89 | 27 | OXY, HEM |
| 3 | 239 | 0.73 | 0.87 | 28 | OXY, HEM |
| 4 | 189 | 0.70 | 0.87 | 25 | OXY, HEM |
| 5 | 206 | 0.70 | 0.86 | 24 | OXY, HEM |
Interfaces
6 interfaces between chains.
- C–D · 902 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 887 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 465 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 436 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 392 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1QXE · Structural Basis for the Potent Antisickling Effect of a Novel Class of 5-Membered… · 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 P69905
- Every structure of UniProt P68871
- Elsewhere: RCSB PDB 1QXE · PDBe 1QXE · UniProt P69905 · UniProt P68871
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