MolNFT v1 · #75168 · protein
Site-specific glycosylation of hemoglobin utilizing oxime ligation chemistry as a viable alternative to pegylation
3PI9 · Hemoglobin subunit alpha: “Site-specific glycosylation of hemoglobin utilizing oxime ligation chemistry as a viable alternative to…”. X-ray diffraction, 2 ligands (HEM, CMO), 8 pockets (best druggability 0.82). MolNFT v1 #75168 on…
- PDB
- 3PI9
- Type
- protein
- Length
- 572 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta
- UniProt
- P01966, P02070
- Ligands
- HEM, CMO
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha | protein | 141 | 77% helix, 0% strand | P01966 |
| B, D | Hemoglobin subunit beta | protein | 145 | 80% helix, 0% strand | P02070 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- CMO · Carbon monoxide · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 495 | 0.82 | 0.89 | 75 | empty |
| 2 | 235 | 0.75 | 0.88 | 37 | HEM, CMO |
| 3 | 179 | 0.72 | 0.89 | 24 | HEM, CMO |
| 4 | 188 | 0.71 | 0.88 | 30 | HEM, CMO |
| 5 | 234 | 0.70 | 0.85 | 30 | HEM, CMO |
Interfaces
6 interfaces between chains.
- A–B · 929 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 896 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 456 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 446 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 415 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3PI9 · Site-specific Glycosylation of Hemoglobin Utilizing Oxime Ligation Chemistry as a Viable… · the same entry in another collection · chain A against A, TM-score 1.00
- P02070 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P02070) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P01966 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha (P01966) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P01966
- Every structure of UniProt P02070
- Elsewhere: RCSB PDB 3PI9 · PDBe 3PI9 · UniProt P01966 · UniProt P02070
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