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Crystal structure of deoxygenated hemoglobin in complex with sphingosine phosphate and 2,3-bisphosphoglycerate
Analyse Crystal structure of deoxygenated hemoglobin in complex with sphingosine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KSI
- 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
- S1P, HEM, DG2
- Pockets
- 10 · best druggability 0.77
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 | 78% helix, 0% strand | P69905 |
| B, D | Hemoglobin subunit beta | protein | 146 | 79% helix, 0% strand | P68871 |
Ligands and binding sites
- S1P · (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate · ligand · 5 copies · chains A, B, D, C
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- DG2 · (2R)-2,3-diphosphoglyceric acid · ligand · 2 copies · chains B, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 638 | 0.77 | 0.83 | 64 | S1P |
| 2 | 230 | 0.73 | 0.87 | 32 | HEM |
| 3 | 218 | 0.72 | 0.87 | 29 | HEM |
| 4 | 280 | 0.71 | 0.85 | 36 | HEM, S1P |
| 5 | 281 | 0.70 | 0.84 | 34 | HEM, S1P |
Interfaces
6 interfaces between chains.
- C–D · 852 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 842 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 711 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 706 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 280 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5KSI · Crystal structure of deoxygenated hemoglobin in complex with sphingosine phosphate and… · 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 5KSI · PDBe 5KSI · UniProt P69905 · UniProt P68871
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