MolNFT v1 · #160723 · protein
Crystal structure of PSS1_19B C77S in complex with kappa-neocarrabiose
6PSM · Exo-4S-kappa carrageenan S1 sulfatase: “Crystal structure of PSS1_19B C77S in complex with kappa-neocarrabiose”. X-ray diffraction, 5 ligands (G4S, 9RN, CA), 20 pockets (best druggability 0.78). MolNFT v1 #160723 on GenesisL1: 3D…
- PDB
- 6PSM
- Type
- protein
- Length
- 2,680 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exo-4S-kappa carrageenan S1 sulfatase
- Ligands
- G4S, 9RN, CA, ZN, CL
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Exo-4S-kappa carrageenan S1 sulfatase | protein | 447 | 34% helix, 17% strand | — |
| C, E | Exo-4S-kappa carrageenan S1 sulfatase | protein | 448 | 33% helix, 17% strand | — |
| D | Exo-4S-kappa carrageenan S1 sulfatase | protein | 444 | 32% helix, 17% strand | — |
| F | Exo-4S-kappa carrageenan S1 sulfatase | protein | 446 | 33% helix, 17% strand | — |
Ligands and binding sites
- G4S · 4-O-sulfo-beta-D-galactopyranose · ligand · 6 copies · chains A, B, C, D, E, F
- 9RN · 3,6-anhydro-alpha-D-galactopyranose · ligand · 6 copies · chains A, B, C, D, E, F
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 6 copies · chains A, D, E
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.78 | 0.98 | 34 | empty |
| 2 | 77 | 0.74 | 0.98 | 26 | empty |
| 3 | 70 | 0.72 | 0.98 | 24 | empty |
| 4 | 250 | 0.67 | 0.84 | 43 | CL, G4S, 9RN |
| 5 | 246 | 0.67 | 0.84 | 44 | CL, G4S, 9RN |
Interfaces
9 interfaces between chains.
- D–F · 1532 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1498 Ų buried · 30 hydrogen bonds · protein-protein
- C–E · 1492 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 316 Ų buried · 5 hydrogen bonds · protein-protein
- C–F · 198 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6PSM · Crystal structure of PsS1_19B C77S in complex with kappa-neocarrabiose · 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 6PSM · PDBe 6PSM
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