MolNFT v1 · #124386 · protein
Deoxyhemoglobin in complex with an aryloxyalkanoic acid
5KDQ · Hemoglobin subunit alpha: “Deoxyhemoglobin in complex with an aryloxyalkanoic acid”. X-ray diffraction, 3 ligands (HEM, KOH, PO4), 11 pockets (best druggability 0.80). MolNFT v1 #124386 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5KDQ
- 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, KOH, PO4
- Pockets
- 11 · best druggability 0.80
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 | 79% 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
- KOH · 3-[2-chloranyl-4-(1~{H}-imidazol-2-yl)phenoxy]propanoic acid · ligand · chains A, C, D
- PO4 · Phosphate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 720 | 0.80 | 0.84 | 77 | KOH |
| 2 | 226 | 0.72 | 0.87 | 31 | HEM |
| 3 | 261 | 0.72 | 0.86 | 37 | HEM |
| 4 | 199 | 0.71 | 0.87 | 26 | HEM |
| 5 | 253 | 0.71 | 0.85 | 33 | HEM |
Interfaces
6 interfaces between chains.
- C–D · 902 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 818 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 727 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 717 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 301 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5KDQ · Deoxyhemoglobin in Complex with an Aryloxyalkanoic acid · the same entry in another collection · chain B against B, 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 5KDQ · PDBe 5KDQ · UniProt P69905 · UniProt P68871
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