Research workbench
The crystal structure of human deoxyhaemoglobin at 1.74 ångströms resolution
Analyse The crystal structure of human deoxyhaemoglobin at 1.74 ångströms resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HHB
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin (deoxy) (alpha chain); Hemoglobin (deoxy) (beta chain)
- UniProt
- P01922, P02023
- Ligands
- HEM, PO4
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin (deoxy) (alpha chain) | protein | 141 | 78% helix, 0% strand | P01922 |
| B, D | Hemoglobin (deoxy) (beta chain) | protein | 146 | 81% helix, 0% strand | P02023 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 2 copies · chains B, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.82 | 0.83 | 89 | empty |
| 2 | 255 | 0.75 | 0.88 | 29 | HEM |
| 3 | 211 | 0.74 | 0.89 | 30 | HEM |
| 4 | 230 | 0.73 | 0.87 | 30 | HEM |
| 5 | 267 | 0.73 | 0.86 | 31 | HEM |
Interfaces
5 interfaces between chains.
- A–B · 847 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 847 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 716 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 716 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 303 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3HHB · The crystal structure of human deoxyhaemoglobin at 1.74 ångströms resolution · the same entry in another collection · chain D against D, 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 P01922
- Every structure of UniProt P02023
- Elsewhere: RCSB PDB 3HHB · PDBe 3HHB · UniProt P01922 · UniProt P02023
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