Research workbench
1.25A resolution crystal structure of human hemoglobin in the oxy form
Analyse 1.25A resolution crystal structure of human hemoglobin in the oxy form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DN1
- Type
- protein
- Length
- 285 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin alpha subunit; Hemoglobin beta subunit
- UniProt
- P69905, P68871
- Ligands
- HEM, MBN, OXY
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemoglobin alpha subunit | protein | 140 | 79% helix, 0% strand | P69905 |
| B | Hemoglobin beta subunit | protein | 145 | 77% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- MBN · Toluene · ligand · 2 copies · chains A
- OXY · Oxygen molecule · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.79 | 0.96 | 19 | MBN |
| 2 | 222 | 0.74 | 0.88 | 28 | HEM, OXY |
| 3 | 197 | 0.70 | 0.86 | 24 | HEM, OXY |
| 4 | 119 | 0.52 | 0.81 | 21 | empty |
| 5 | 75 | 0.39 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 920 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2DN1 · 1.25A resolution crystal structure of human hemoglobin in the oxy form · 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 2DN1 · PDBe 2DN1 · UniProt P69905 · UniProt P68871
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