Research workbench
MAGNESIUM(II)-and ZINC(II)-protoporphyrin IX'S stabilize the lowest oxygen affinity state of human hemoglobin even more strongly than deoxyheme
Analyse MAGNESIUM(II)-and ZINC(II)-protoporphyrin IX'S stabilize the lowest oxygen… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QSI
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (hemoglobin alpha chain); Protein (hemoglobin beta chain)
- UniProt
- P69905, P68871
- Ligands
- HEM, HEG, CMO
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Protein (hemoglobin alpha chain) | protein | 141 | 78% helix, 0% strand | P69905 |
| B, D | Protein (hemoglobin beta chain) | protein | 146 | 82% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, C
- HEG · Protoporphyrin IX containing Mg · ligand · 2 copies · chains B, D
- CMO · Carbon monoxide · ion · 2 copies · chains A, C
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 | 756 | 0.79 | 0.83 | 74 | empty |
| 2 | 261 | 0.76 | 0.88 | 28 | HEM, CMO |
| 3 | 224 | 0.74 | 0.88 | 30 | HEG |
| 4 | 224 | 0.73 | 0.88 | 30 | HEG |
| 5 | 259 | 0.69 | 0.84 | 29 | HEM, CMO |
Interfaces
5 interfaces between chains.
- C–D · 860 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 837 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 720 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 712 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 305 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1QSI · MAGNESIUM(II)-and ZINC(II)-protoporphyrin IX'S stabilize the lowest oxygen affinity state… · 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 1QSI · PDBe 1QSI · UniProt P69905 · UniProt P68871
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