Research workbench
Crystal structure of a phosphoserine phosphatase (serb) from helicobacter pylori
Analyse Crystal structure of a phosphoserine phosphatase (serb) from helicobacter pylori in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M1Y
- Type
- protein
- Length
- 823 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoserine phosphatase (serb)
- UniProt
- O25367
- Ligands
- MG, CL
- Pockets
- 13 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoserine phosphatase (serb) | protein | 203 | 38% helix, 26% strand | O25367 |
| B | Phosphoserine phosphatase (serb) | protein | 206 | 45% helix, 26% strand | O25367 |
| C | Phosphoserine phosphatase (serb) | protein | 208 | 43% helix, 25% strand | O25367 |
| D | Phosphoserine phosphatase (serb) | protein | 206 | 41% helix, 26% strand | O25367 |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.68 | 0.84 | 34 | MG, CL |
| 2 | 253 | 0.63 | 0.81 | 30 | MG, CL |
| 3 | 266 | 0.62 | 0.81 | 34 | CL |
| 4 | 228 | 0.59 | 0.80 | 36 | MG, CL |
| 5 | 183 | 0.57 | 0.80 | 27 | empty |
Interfaces
3 interfaces between chains.
- C–D · 954 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 928 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 545 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 modified (engineered).
Compared structures
- 3M1Y · Crystal Structure of a Phosphoserine phosphatase (SerB) from Helicobacter pylori · 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 O25367
- Elsewhere: RCSB PDB 3M1Y · PDBe 3M1Y · UniProt O25367
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