MolNFT v1 · #67156 · protein
Crystal structure of liganded hemoglobin in complex with a potent antisickling agent, inn-266
3IC2 · Hemoglobin subunit alpha: “Crystal structure of liganded hemoglobin in complex with a potent antisickling agent, inn-266”. X-ray diffraction, 4 ligands (HEM, B78, OXY), 9 pockets (best druggability 0.83). MolNFT v1 #67156 on…
- PDB
- 3IC2
- 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, B78, OXY, SO4
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 78% 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 | 78% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- B78 · 4-[(5-methoxy-2-methylphenoxy)methyl]pyridine · ligand · 2 copies · chains A, C
- OXY · Oxygen molecule · ion · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 486 | 0.83 | 0.90 | 81 | B78 |
| 2 | 230 | 0.75 | 0.89 | 31 | OXY, HEM |
| 3 | 227 | 0.73 | 0.87 | 28 | OXY, HEM |
| 4 | 196 | 0.71 | 0.87 | 25 | OXY, HEM |
| 5 | 188 | 0.69 | 0.86 | 24 | OXY, HEM |
Interfaces
6 interfaces between chains.
- C–D · 937 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 928 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 456 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 456 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 410 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3IC2 · Crystal Structure of liganded hemoglobin in complex with a potent antisickling agent… · the same entry in another collection · chain D against D, 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 3IC2 · PDBe 3IC2 · UniProt P69905 · UniProt P68871
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