Research workbench
Structure of hba with compound 19
Analyse Structure of hba with compound 19 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JY1
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta
- UniProt
- P69905, P68871
- Ligands
- O4B, HEM, VOP, CMO
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 77% 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 | 146 | 77% helix, 0% strand | P68871 |
Ligands and binding sites
- O4B · 1,4,7,10,13,16-hexaoxacyclooctadecane · ligand · 7 copies · chains A, B, C, D
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- VOP · [6-{(1S)-1-[(2-amino-6-fluoroquinolin-3-yl)oxy]ethyl}-5-(1H-pyrazol-1-yl)-1H-indazol-1-yl]acetic acid · ligand · 2 copies · chains A, C
- CMO · Carbon monoxide · ion · 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 436 | 0.82 | 0.89 | 67 | empty |
| 2 | 208 | 0.73 | 0.88 | 30 | HEM, CMO |
| 3 | 200 | 0.71 | 0.87 | 28 | HEM, CMO |
| 4 | 184 | 0.71 | 0.89 | 41 | empty |
| 5 | 188 | 0.71 | 0.87 | 23 | HEM, CMO |
Interfaces
6 interfaces between chains.
- C–D · 967 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 944 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 475 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 448 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 404 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7JY1 · Structure of HbA with compound 19 · the same entry in another collection · chain D against D, TM-score 1.00
- P68871 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P68871) · a predicted model of the same protein · chain D against A, TM-score 0.98
- P69905 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha (P69905) · a predicted model of the same protein · chain C 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 7JY1 · PDBe 7JY1 · UniProt P69905 · UniProt P68871
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