Research workbench
Structure of deoxy-quaternary haemoglobin with liganded beta subunits
Analyse Structure of deoxy-quaternary haemoglobin with liganded beta subunits in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NIH
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Homo sapiens
- Molecule
- Hemoglobin (nickelous deoxy) (alpha chain); Hemoglobin (ferrous carbonmonoxy) (beta chain)
- UniProt
- P69905, P68871
- Ligands
- HNI, HEM, IHP, CMO
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.6 · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin (nickelous deoxy) (alpha chain) | protein | 141 | 77% helix, 0% strand | P69905 |
| B, D | Hemoglobin (ferrous carbonmonoxy) (beta chain) | protein | 146 | 80% helix, 0% strand | P68871 |
Ligands and binding sites
- HNI · Protoporphyrin IX containing ni(ii) · ligand · 2 copies · chains A, C
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains B, D
- IHP · Inositol hexakisphosphate · ligand · chains B, D
- CMO · Carbon monoxide · ion · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 668 | 0.79 | 0.84 | 68 | empty |
| 2 | 248 | 0.74 | 0.88 | 31 | HEM, CMO |
| 3 | 267 | 0.73 | 0.86 | 32 | HNI |
| 4 | 275 | 0.72 | 0.85 | 29 | HNI |
| 5 | 243 | 0.72 | 0.86 | 27 | HEM, CMO |
Interfaces
5 interfaces between chains.
- A–B · 882 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 850 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 719 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 711 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 289 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1NIH · Structure of deoxy-quaternary haemoglobin with liganded beta subunits · the same entry in another collection · chain A against A, TM-score 1.00
- P69905 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha (P69905) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P68871 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P68871) · 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 P69905
- Every structure of UniProt P68871
- Elsewhere: RCSB PDB 1NIH · PDBe 1NIH · UniProt P69905 · UniProt P68871
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