MolNFT v1 · #144245 · protein
Carbonmonoxy hemoglobin in complex with the antisickling agent 5- methoxy-2-(pyridin-2-YLMETHOXY)BENZALDEHYDE (INN310)
6BNR · Hemoglobin subunit alpha: “Carbonmonoxy hemoglobin in complex with the antisickling agent 5- methoxy-2-(pyridin-2-YLMETHOXY)BENZALDEHYDE…”. X-ray diffraction, 3 ligands (HEM, E0J, CMO), 6 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 6BNR
- 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, E0J, CMO
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha | protein | 141 | 74% helix, 0% strand | P69905 |
| B, D | Hemoglobin subunit beta | protein | 146 | 77% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- E0J · 2-[(4-methoxy-2-methylphenoxy)methyl]pyridine · ligand · 2 copies · chains A, C
- CMO · Carbon monoxide · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.82 | 0.90 | 69 | empty |
| 2 | 232 | 0.74 | 0.88 | 28 | CMO, HEM |
| 3 | 206 | 0.73 | 0.88 | 27 | CMO, HEM |
| 4 | 181 | 0.69 | 0.86 | 23 | CMO, HEM |
| 5 | 180 | 0.69 | 0.86 | 24 | CMO, HEM |
Interfaces
6 interfaces between chains.
- A–B · 907 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 906 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 472 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 419 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 411 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6BNR · Carbonmonoxy hemoglobin in complex with the antisickling agent… · 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 6BNR · PDBe 6BNR · UniProt P69905 · UniProt P68871
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