MolNFT v1 · #34126 · protein
Hemoglobin alpha subunit and Hemoglobin beta subunit
2D60 · Hemoglobin alpha subunit and Hemoglobin beta subunit. X-ray diffraction, 2 ligands (HEM, L35), 10 pockets (best druggability 0.81). MolNFT v1 #34126 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2D60
- Type
- protein
- Length
- 572 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin alpha subunit; Hemoglobin beta subunit
- UniProt
- P69905, P68871
- Ligands
- HEM, L35
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin alpha subunit | protein | 141 | 78% helix, 0% strand | P69905 |
| B, D | Hemoglobin beta subunit | protein | 145 | 77% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- L35 · 2-[4-({[(3,5-dichlorophenyl)amino]carbonyl}amino)phenoxy]-2-methylpropanoic acid · ligand · 2 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 857 | 0.81 | 0.83 | 73 | L35 |
| 2 | 235 | 0.74 | 0.88 | 30 | HEM |
| 3 | 211 | 0.74 | 0.88 | 30 | HEM |
| 4 | 189 | 0.71 | 0.87 | 28 | HEM |
| 5 | 219 | 0.70 | 0.86 | 29 | HEM |
Interfaces
6 interfaces between chains.
- A–B · 844 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 836 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 728 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 723 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 330 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2D60 · Crystal structure of deoxy human hemoglobin complexed with two L35 molecules · 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 2D60 · PDBe 2D60 · UniProt P69905 · UniProt P68871
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