Research workbench
Crystal structure of PSS1_19B C77S in complex with iota- neocarratetraose
Analyse Crystal structure of PSS1_19B C77S in complex with iota- neocarratetraose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PSO
- Type
- protein
- Length
- 894 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exo-4S-kappa carrageenan S1 sulfatase
- Ligands
- G4S, DGS, CA, CL
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Exo-4S-kappa carrageenan S1 sulfatase | protein | 447 | 33% helix, 17% strand | — |
Ligands and binding sites
- G4S · 4-O-sulfo-beta-D-galactopyranose · ligand · 4 copies · chains B, A
- DGS · 3,6-anhydro-2-O-sulfo-alpha-D-galactopyranose · ligand · 4 copies · chains B, A
- CA · Calcium ion · metal · 2 copies · chains B, A
- CL · Chloride ion · ion · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.77 | 0.98 | 29 | empty |
| 2 | 338 | 0.66 | 0.81 | 40 | G4S, DGS, CL |
| 3 | 292 | 0.66 | 0.81 | 36 | G4S, DGS |
| 4 | 237 | 0.55 | 0.77 | 33 | empty |
| 5 | 93 | 0.44 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- B–A · 1524 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6PSO · Crystal structure of PsS1_19B C77S in complex with iota-neocarratetraose · 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
- Elsewhere: RCSB PDB 6PSO · PDBe 6PSO
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