MolNFT v1 · #83415 · protein
Structure of hemoglobin complex with 18-crown-6
3WHM · Hemoglobin subunit alpha: “Structure of hemoglobin complex with 18-crown-6”. X-ray diffraction, 3 ligands (O4B, HEM, OXY), 8 pockets (best druggability 0.83). MolNFT v1 #83415 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3WHM
- Type
- protein
- Length
- 566 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, OXY
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Hemoglobin subunit alpha | protein | 140 | 76% helix, 0% strand | P69905 |
| B, F | Hemoglobin subunit beta | protein | 143 | 78% helix, 0% strand | P68871 |
Ligands and binding sites
- O4B · 1,4,7,10,13,16-hexaoxacyclooctadecane · ligand · 5 copies · chains A, B, E, F
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, E, F
- OXY · Oxygen molecule · ion · 3 copies · chains A, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 729 | 0.83 | 0.86 | 90 | empty |
| 2 | 209 | 0.74 | 0.89 | 27 | HEM, OXY |
| 3 | 216 | 0.72 | 0.87 | 28 | HEM, OXY |
| 4 | 176 | 0.69 | 0.87 | 23 | HEM, OXY |
| 5 | 183 | 0.67 | 0.85 | 24 | HEM |
Interfaces
6 interfaces between chains.
- A–B · 867 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 861 Ų buried · 11 hydrogen bonds · protein-protein
- A–F · 465 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 425 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 363 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3WHM · Structure of Hemoglobin Complex with 18-crown-6 · 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 3WHM · PDBe 3WHM · UniProt P69905 · UniProt P68871
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