MolNFT v1 · #135587 · protein
Crystal structure of carbonmonoxy hemoglobin S (liganded sickle cell hemoglobin) complexed with gbt compound 31
5U3I · Hemoglobin subunit alpha: “Crystal structure of carbonmonoxy hemoglobin S (liganded sickle cell hemoglobin) complexed with gbt compound…”. X-ray diffraction, 3 ligands (HEM, 7SJ, CMO), 6 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 5U3I
- Type
- protein
- Length
- 573 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, 7SJ, CMO
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha | protein | 141 | 78% helix, 0% strand | P69905 |
| B | Hemoglobin subunit beta | protein | 146 | 79% helix, 0% strand | P68871 |
| D | Hemoglobin subunit beta | protein | 145 | 81% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- 7SJ · 2-methoxy-5-({2-[1-(propan-2-yl)-1H-pyrazol-5-yl]pyridin-3-yl}methoxy)pyridine-4-carbaldehyde · ligand · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1159 | 0.85 | 0.86 | 114 | 7SJ |
| 2 | 223 | 0.74 | 0.88 | 29 | HEM, CMO |
| 3 | 230 | 0.73 | 0.87 | 30 | HEM, CMO |
| 4 | 219 | 0.72 | 0.87 | 28 | HEM, CMO |
| 5 | 237 | 0.71 | 0.86 | 29 | HEM, CMO |
Interfaces
6 interfaces between chains.
- A–B · 935 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 934 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 459 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 451 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 366 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5U3I · CRYSTAL STRUCTURE OF CARBONMONOXY HEMOGLOBIN S (LIGANDED SICKLE CELL HEMOGLOBIN)… · 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 5U3I · PDBe 5U3I · UniProt P69905 · UniProt P68871
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