Research workbench
Crystal structure of PSS1_NC C84S in complex with I-neocarratetraose
Analyse Crystal structure of PSS1_NC C84S in complex with I-neocarratetraose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PT6
- Type
- protein
- Length
- 945 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exo-2S-iota carrageenan S1 sulfatase
- Ligands
- G4S, DGS, CA
- Pockets
- 10 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Exo-2S-iota carrageenan S1 sulfatase | protein | 472 | 36% helix, 19% strand | — |
| A | Exo-2S-iota carrageenan S1 sulfatase | protein | 473 | 36% helix, 18% strand | — |
Ligands and binding sites
- G4S · 4-O-sulfo-beta-D-galactopyranose · ligand · 2 copies · chains B, A
- DGS · 3,6-anhydro-2-O-sulfo-alpha-D-galactopyranose · ligand · 2 copies · chains B, A
- CA · Calcium ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.68 | 0.79 | 72 | empty |
| 2 | 522 | 0.67 | 0.78 | 49 | G4S, DGS |
| 3 | 477 | 0.67 | 0.78 | 46 | G4S, DGS |
| 4 | 210 | 0.58 | 0.80 | 43 | empty |
| 5 | 139 | 0.52 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- B–A · 1610 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 6PT6 · Crystal structure of PsS1_NC C84S in complex with i-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 6PT6 · PDBe 6PT6
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