Research workbench
Crystal structure of deoxygenated hemoglobin in complex with 5HMF-no at 1.8 ångström
Analyse Crystal structure of deoxygenated hemoglobin in complex with 5HMF-no at 1.8… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UD7
- 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, MWC
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha | protein | 141 | 78% helix, 0% strand | P69905 |
| B, D | Hemoglobin subunit beta | protein | 146 | 80% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- MWC · dihydroxy[(5-methylfuran-2-yl)methoxy]amine · ligand · 2 copies · chains A, B, C, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 668 | 0.79 | 0.84 | 64 | MWC |
| 2 | 206 | 0.74 | 0.89 | 29 | HEM |
| 3 | 243 | 0.73 | 0.87 | 29 | HEM |
| 4 | 202 | 0.72 | 0.88 | 26 | HEM |
| 5 | 245 | 0.70 | 0.85 | 28 | HEM |
Interfaces
6 interfaces between chains.
- C–D · 864 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 833 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 728 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 717 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 314 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7UD7 · Crystal structure of deoxygenated hemoglobin in complex with 5HMF-NO at 1.8 Angstrom · the same entry in another collection · chain D against D, TM-score 1.00
- P69905 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha (P69905) · a predicted model of the same protein · chain C against A, 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
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 7UD7 · PDBe 7UD7 · UniProt P69905 · UniProt P68871
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