Research workbench
Structure of the S. agalactiae SERINE/THREONINE phosphatase at 2.65 resolution
Analyse Structure of the S. agalactiae SERINE/THREONINE phosphatase at 2.65 resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PK0
- Type
- protein
- Length
- 979 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE protein phosphatase STP1
- EC
- 3.1.3.16
- UniProt
- Q3K363
- Ligands
- MG, CL
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | SERINE/THREONINE protein phosphatase STP1 (EC 3.1.3.16) | protein | 247 | 32% helix, 29% strand | Q3K363 |
| C | SERINE/THREONINE protein phosphatase STP1 (EC 3.1.3.16) | protein | 242 | 33% helix, 30% strand | Q3K363 |
| D | SERINE/THREONINE protein phosphatase STP1 (EC 3.1.3.16) | protein | 243 | 34% helix, 30% strand | Q3K363 |
Ligands and binding sites
- MG · Magnesium ion · metal · 10 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains C, D
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 965 | 0.73 | 0.77 | 92 | MG |
| 2 | 548 | 0.71 | 0.80 | 67 | MG |
| 3 | 255 | 0.53 | 0.76 | 34 | MG |
| 4 | 263 | 0.51 | 0.75 | 37 | empty |
| 5 | 51 | 0.27 | 0.75 | 13 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1120 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 382 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 266 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 121 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2PK0 · Structure of the S. agalactiae serine/threonine phosphatase at 2.65 resolution · 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 Q3K363
- Elsewhere: RCSB PDB 2PK0 · PDBe 2PK0 · UniProt Q3K363
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