Research workbench
Glycation restrains allosteric transition in hemoglobin: the molecular basis of oxidative stress under hyperglycemic conditions in diabetes
Analyse Glycation restrains allosteric transition in hemoglobin: the molecular basis of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HY8
- Type
- protein
- Length
- 1,428 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta
- UniProt
- P69905, P68871
- Ligands
- HEM, FRU, GLC, OXY
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, S | Hemoglobin subunit alpha | protein | 141 | 77% helix, 0% strand | P69905 |
| B, D, F, H, T | Hemoglobin subunit beta | protein | 146 | 80% helix, 0% strand | P68871 |
| E | Hemoglobin subunit alpha | protein | 137 | 80% helix, 0% strand | P69905 |
| G | Hemoglobin subunit alpha | protein | 138 | 79% helix, 0% strand | P69905 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 10 copies · chains A, B, C, D, E, F, G, H, S, T
- FRU · beta-D-fructofuranose · sugar · 3 copies · chains A, D, B, C, F, H
- GLC · alpha-D-glucopyranose · sugar · chains C
- OXY · Oxygen molecule · ion · 8 copies · chains A, B, C, D, F, G, S, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 739 | 0.84 | 0.87 | 74 | empty |
| 2 | 447 | 0.81 | 0.89 | 72 | empty |
| 3 | 241 | 0.75 | 0.88 | 29 | HEM, OXY |
| 4 | 227 | 0.74 | 0.88 | 28 | HEM, OXY |
| 5 | 229 | 0.73 | 0.87 | 29 | HEM |
Interfaces
16 interfaces between chains.
- A–B · 971 Ų buried · 11 hydrogen bonds · protein-protein
- S–T · 951 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 907 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 900 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 887 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 glycan (glycation).
Compared structures
- 5HY8 · Glycation restrains allosteric transition in hemoglobin: The molecular basis of oxidative… · 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 5HY8 · PDBe 5HY8 · UniProt P69905 · UniProt P68871
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