Research workbench
R2-state HbG-Makassar hemoglobin
Analyse R2-state HbG-Makassar hemoglobin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 9AV9
- Type
- protein
- Length
- 570 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.94
- Source
- Homo sapiens
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta
- UniProt
- P69905, P68871
- Ligands
- HEM
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · resolution 1.94 · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha | protein | 141 | 77% helix, 0% strand | P69905 |
| B, D | Hemoglobin subunit beta | protein | 144 | 76% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 818 | 0.84 | 0.87 | 91 | GOL |
| 2 | 222 | 0.73 | 0.88 | 27 | HEM |
| 3 | 211 | 0.73 | 0.88 | 29 | HEM |
| 4 | 182 | 0.69 | 0.87 | 24 | HEM |
| 5 | 201 | 0.69 | 0.86 | 25 | HEM |
Interfaces
5 interfaces between chains.
- A–B · 924 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 906 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 475 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 451 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 389 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- P68871 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P68871) · a predicted model of the same protein · chain D against A, TM-score 0.99
- P69905 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha (P69905) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 9AV9 · PDBe 9AV9 · UniProt P69905 · UniProt P68871
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