Research workbench
1.25A resolution crystal structure of human hemoglobin in the carbonmonoxy form
Analyse 1.25A resolution crystal structure of human hemoglobin in the carbonmonoxy form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DN3
- Type
- protein
- Length
- 287 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, CMO
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemoglobin alpha subunit | protein | 141 | 76% helix, 0% strand | P69905 |
| B | Hemoglobin beta subunit | protein | 146 | 77% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- CMO · Carbon monoxide · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.73 | 0.88 | 27 | HEM, CMO |
| 2 | 200 | 0.69 | 0.85 | 26 | HEM, CMO |
| 3 | 123 | 0.51 | 0.81 | 23 | empty |
| 4 | 83 | 0.40 | 0.78 | 21 | empty |
| 5 | 85 | 0.34 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 935 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2DN3 · 1.25A resolution crystal structure of human hemoglobin in the carbonmonoxy 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 2DN3 · PDBe 2DN3 · UniProt P69905 · UniProt P68871
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