Research workbench
Deoxyhemoglobin in complex with imidazolylacryloyl derivatives
Analyse Deoxyhemoglobin in complex with imidazolylacryloyl derivatives in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ROM
- 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
- HEM, 3U8, SO4
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha | protein | 141 | 74% helix, 0% strand | P69905 |
| B, D | Hemoglobin subunit beta | protein | 146 | 75% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- 3U8 · 4-{2-chloro-4-[3-(1H-imidazol-2-yl)propanoyl]phenoxy}butanoic acid · ligand · 2 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.81 | 0.83 | 83 | 3U8 |
| 2 | 207 | 0.73 | 0.88 | 30 | HEM |
| 3 | 238 | 0.73 | 0.87 | 30 | HEM |
| 4 | 196 | 0.72 | 0.88 | 27 | HEM |
| 5 | 235 | 0.69 | 0.84 | 29 | HEM |
Interfaces
6 interfaces between chains.
- C–D · 866 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 835 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 727 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 713 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 335 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4ROM · Deoxyhemoglobin in complex with imidazolylacryloyl derivatives · 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 4ROM · PDBe 4ROM · UniProt P69905 · UniProt P68871
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