Research workbench
Structure of saposin B in complex with chloroquine
Analyse Structure of saposin B in complex with chloroquine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4V2O
- Type
- protein
- Length
- 240 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Saposin-B
- UniProt
- P07602
- Ligands
- CLQ
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 82% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Saposin-B | protein | 78 | 82% helix, 0% strand | P07602 |
| B, C | Saposin-B | protein | 81 | 81% helix, 0% strand | P07602 |
Ligands and binding sites
- CLQ · N4-(7-chloro-quinolin-4-yl)-N1,N1-diethyl-pentane-1,4-diamine · ligand · 2 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 880 | 0.74 | 0.77 | 50 | empty |
| 2 | 137 | 0.41 | 0.75 | 20 | empty |
| 3 | 143 | 0.41 | 0.73 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–C · 931 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 66 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
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 P07602
- Elsewhere: RCSB PDB 4V2O · PDBe 4V2O · UniProt P07602
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