Research workbench
A novel allosteric mechanism in haemoglobin. structure of bovine deoxyhaemoglobin, absence of specific chloride-binding sites and origin of the chloride-linked bohr effect in bovine and human haemoglobin
Analyse A novel allosteric mechanism in haemoglobin. structure of bovine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HDA
- Type
- protein
- Length
- 572 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
- P01966, P02070
- Ligands
- HEM
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin (deoxy) (alpha chain) | protein | 141 | 76% helix, 0% strand | P01966 |
| B, D | Hemoglobin (deoxy) (beta chain) | protein | 145 | 78% helix, 0% strand | P02070 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 742 | 0.80 | 0.84 | 73 | empty |
| 2 | 229 | 0.75 | 0.89 | 28 | HEM |
| 3 | 286 | 0.74 | 0.86 | 33 | HEM |
| 4 | 209 | 0.72 | 0.87 | 27 | HEM |
| 5 | 288 | 0.72 | 0.85 | 35 | HEM |
Interfaces
5 interfaces between chains.
- A–B · 859 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 857 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 727 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 717 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 321 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1HDA · A novel allosteric mechanism in haemoglobin. structure of bovine deoxyhaemoglobin… · the same entry in another collection · chain A against A, TM-score 1.00
- P01966 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha (P01966) · a predicted model of the same protein · 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 0.99
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 1HDA · PDBe 1HDA · UniProt P01966 · UniProt P02070
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