Research workbench
Crystal structure of putative phosphatase (DUF442) (YP_001181608.1) from shewanella putrefaciens cn-32 at 1.60 a resolution
Analyse Crystal structure of putative phosphatase (DUF442) (YP_001181608.1) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GXG
- Type
- protein
- Length
- 628 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative phosphatase (DUF442)
- UniProt
- A4Y1H6
- Ligands
- SO4, CL
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Putative phosphatase (DUF442) | protein | 157 | 43% helix, 13% strand | A4Y1H6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D
- CL · Chloride ion · ion · 6 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, C, B, D
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 696 | 0.72 | 0.79 | 72 | CL, EDO |
| 2 | 110 | 0.42 | 0.77 | 28 | empty |
| 3 | 52 | 0.31 | 0.77 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1009 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1000 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 418 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 105 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 30 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3GXG · Crystal structure of Putative phosphatase (DUF442) (YP_001181608.1) from SHEWANELLA… · 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 A4Y1H6
- Elsewhere: RCSB PDB 3GXG · PDBe 3GXG · UniProt A4Y1H6
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