Research workbench
Mammalian blood serum haemopexin glycosylated-native protein and in complex with its ligand haem
Analyse Mammalian blood serum haemopexin glycosylated-native protein and in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QJS
- Type
- protein
- Length
- 816 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemopexin
- UniProt
- P20058
- Ligands
- HEM, NA, CL, PO4
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hemopexin | protein | 408 | 10% helix, 37% strand | P20058 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 8 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1020 | 0.71 | 0.75 | 95 | PO4 |
| 2 | 259 | 0.60 | 0.80 | 45 | empty |
| 3 | 392 | 0.60 | 0.76 | 35 | HEM |
| 4 | 170 | 0.59 | 0.83 | 24 | empty |
| 5 | 308 | 0.58 | 0.77 | 34 | HEM |
Interfaces
1 interface between chains.
- A–B · 847 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 1QJS · mammalian blood serum haemopexin glycosylated-native protein and in complex with its… · 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 1QJS · PDBe 1QJS · UniProt P20058
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