Research workbench
Mammalian blood serum haemopexin deglycosylated and in complex with its ligand haem
Analyse Mammalian blood serum haemopexin deglycosylated and in complex with its ligand… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QHU
- Type
- protein
- Length
- 398 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (hemopexin)
- UniProt
- P20058
- Ligands
- HEM, NA, CL, PO4
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (hemopexin) | protein | 398 | 11% helix, 38% strand | P20058 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- NA · Sodium ion · metal · 4 copies · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 240 | 0.59 | 0.80 | 43 | empty |
| 2 | 296 | 0.53 | 0.74 | 33 | HEM |
| 3 | 75 | 0.37 | 0.77 | 17 | empty |
| 4 | 65 | 0.34 | 0.76 | 13 | empty |
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1QHU · Mammalian blood serum haemopexin deglycosylated and in complex with its ligand haem · the same entry in another collection · chain A against A, TM-score 1.00
- P20058 · AlphaFold monomer V2.0 prediction for hemopexin (P20058) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P20058
- Elsewhere: RCSB PDB 1QHU · PDBe 1QHU · UniProt P20058
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