Research workbench
Structure determination of the double mutant S233Y F250G from the sec-alkyl sulfatase PISA1
Analyse Structure determination of the double mutant S233Y F250G from the sec-alkyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AV7
- Type
- protein
- Length
- 3,807 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sec-alkylsulfatase
- UniProt
- F8KAY7
- Ligands
- ZN, SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F | Sec-alkylsulfatase | protein | 634 | 43% helix, 17% strand | F8KAY7 |
| B | Sec-alkylsulfatase | protein | 637 | 41% helix, 17% strand | F8KAY7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 541 | 0.87 | 0.92 | 40 | empty |
| 2 | 540 | 0.86 | 0.92 | 40 | empty |
| 3 | 528 | 0.86 | 0.92 | 40 | empty |
| 4 | 691 | 0.81 | 0.86 | 71 | empty |
| 5 | 447 | 0.81 | 0.89 | 45 | empty |
Interfaces
11 interfaces between chains.
- B–C · 5094 Ų buried · 81 hydrogen bonds · protein-protein
- A–D · 5093 Ų buried · 75 hydrogen bonds · protein-protein
- E–F · 5071 Ų buried · 76 hydrogen bonds · protein-protein
- A–B · 691 Ų buried · 3 hydrogen bonds · protein-protein
- C–F · 688 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4AV7 · Structure determination of the double mutant S233Y F250G from the sec- alkyl sulfatase… · 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
- Every structure of UniProt F8KAY7
- Elsewhere: RCSB PDB 4AV7 · PDBe 4AV7 · UniProt F8KAY7
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