MolNFT v1 · #160756 · protein
Crystal structure of the sulfatase PSS1_NC C84A with bound sulfate ion
6PTK · Exo-2S-iota carrageenan S1 sulfatase: “Crystal structure of the sulfatase PSS1_NC C84A with bound sulfate ion”. X-ray diffraction, 4 ligands (9RN, G4S, CA), 18 pockets (best druggability 0.76). MolNFT v1 #160756 on GenesisL1: 3D…
- PDB
- 6PTK
- Type
- protein
- Length
- 1,887 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exo-2S-iota carrageenan S1 sulfatase
- Ligands
- 9RN, G4S, CA, SO4
- Pockets
- 18 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Exo-2S-iota carrageenan S1 sulfatase | protein | 472 | 36% helix, 19% strand | — |
| D | Exo-2S-iota carrageenan S1 sulfatase | protein | 471 | 36% helix, 19% strand | — |
Ligands and binding sites
- 9RN · 3,6-anhydro-alpha-D-galactopyranose · ligand · 4 copies · chains A, B, C, D
- G4S · 4-O-sulfo-beta-D-galactopyranose · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 14 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, C, D
- GOL · Glycerol · additive · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.76 | 0.79 | 80 | GOL, G4S |
| 2 | 740 | 0.75 | 0.80 | 63 | empty |
| 3 | 498 | 0.67 | 0.78 | 56 | SO4, GOL, CA |
| 4 | 495 | 0.66 | 0.78 | 59 | SO4, EDO, GOL, CA |
| 5 | 433 | 0.65 | 0.78 | 47 | SO4, EDO, GOL |
Interfaces
4 interfaces between chains.
- C–D · 350 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 341 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 119 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 109 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6PTK · Crystal structure of the sulfatase PsS1_NC C84A with bound sulfate ion · the same entry in another collection · chain A against A, 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 6PTK · PDBe 6PTK
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