MolNFT v1 · #58550 · protein
Crystal structure of glycated human haemoglobin
3B75 · Hemoglobin subunit alpha: “Crystal structure of glycated human haemoglobin”. X-ray diffraction, 5 ligands (HEM, GLC, FRU), 20 pockets (best druggability 0.82). MolNFT v1 #58550 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3B75
- Type
- protein
- Length
- 1,435 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, GLC, FRU, OXY, PO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, S | Hemoglobin subunit alpha | protein | 141 | 72% helix, 0% strand | P69905 |
| B, D, F, H, T | Hemoglobin subunit beta | protein | 146 | 77% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 10 copies · chains A, B, C, D, E, F, G, H, S, T
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains B, C, S, T
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains A, B, C, D, E, F, G, H
- OXY · Oxygen molecule · ion · 10 copies · chains A, B, C, D, E, F, G, H, S, T
- PO4 · Phosphate ion · ion · chains E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.82 | 0.89 | 79 | FRU |
| 2 | 232 | 0.76 | 0.89 | 27 | HEM, OXY |
| 3 | 227 | 0.73 | 0.87 | 28 | HEM, OXY |
| 4 | 243 | 0.73 | 0.86 | 28 | HEM, OXY |
| 5 | 238 | 0.73 | 0.87 | 28 | HEM, OXY |
Interfaces
16 interfaces between chains.
- S–T · 961 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 949 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 948 Ų buried · 8 hydrogen bonds · protein-protein
- G–H · 932 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 930 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan (glycation).
Compared structures
- 3B75 · Crystal Structure of Glycated Human Haemoglobin · 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 3B75 · PDBe 3B75 · UniProt P69905 · UniProt P68871
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