Research workbench
Crystal structure of putative arylsulfatase from escherichia COLI
Analyse Crystal structure of putative arylsulfatase from escherichia COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ED4
- Type
- protein
- Length
- 1,883 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arylsulfatase
- UniProt
- Q8FLC3
- Ligands
- UNL, NA, SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arylsulfatase | protein | 468 | 29% helix, 16% strand | Q8FLC3 |
| B | Arylsulfatase | protein | 474 | 29% helix, 16% strand | Q8FLC3 |
| C | Arylsulfatase | protein | 467 | 30% helix, 16% strand | Q8FLC3 |
| D | Arylsulfatase | protein | 474 | 30% helix, 16% strand | Q8FLC3 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 6 copies · chains A, B, C, D
- NA · Sodium ion · metal · 6 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.81 | 0.83 | 97 | empty |
| 2 | 180 | 0.81 | 0.96 | 48 | empty |
| 3 | 517 | 0.74 | 0.82 | 75 | SO4 |
| 4 | 530 | 0.71 | 0.80 | 82 | SO4 |
| 5 | 221 | 0.59 | 0.80 | 31 | SO4 |
Interfaces
5 interfaces between chains.
- C–D · 1750 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1741 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 555 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 399 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 326 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3ED4 · Crystal structure of putative arylsulfatase from escherichia coli · 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 Q8FLC3
- Elsewhere: RCSB PDB 3ED4 · PDBe 3ED4 · UniProt Q8FLC3
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