Research workbench
Qauternary R co-liganded hemoglobin structure in complex with a thiol containing compound
Analyse Qauternary R co-liganded hemoglobin structure in complex with a thiol… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NI1
- Type
- protein
- Length
- 285 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta
- UniProt
- P69905, P68871
- Ligands
- 2JX, HEM, MBN, CMO
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemoglobin subunit alpha | protein | 141 | 80% helix, 0% strand | P69905 |
| B | Hemoglobin subunit beta | protein | 144 | 78% helix, 0% strand | P68871 |
Ligands and binding sites
- 2JX · 5-[(2R)-2,3-dihydro-1,4-benzodioxin-2-yl]-2,4-dihydro-3H-1,2,4-triazole-3-thione · ligand · 4 copies · chains A, B
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- MBN · Toluene · ligand · 2 copies · chains A
- CMO · Carbon monoxide · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.79 | 0.95 | 21 | MBN |
| 2 | 201 | 0.73 | 0.89 | 28 | CMO, HEM |
| 3 | 189 | 0.67 | 0.85 | 23 | CMO, HEM |
| 4 | 275 | 0.60 | 0.79 | 34 | 2JX |
| 5 | 54 | 0.36 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 930 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4NI1 · Quaternary R CO-liganded hemoglobin structure in complex with a thiol containing compound · 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 4NI1 · PDBe 4NI1 · UniProt P69905 · UniProt P68871
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