MolNFT v1 · #144594 · protein
Crystal structure of the core catalytic domain of pp-ip phosphatase SIW14 from S. cerevisiae in complex with citrate
6BYF · Tyrosine-protein phosphatase SIW14: “Crystal structure of the core catalytic domain of pp-ip phosphatase SIW14 from S. cerevisiae in complex with…”. X-ray diffraction, 1 ligand (CL), 9 pockets (best druggability 0.89). MolNFT v1…
- PDB
- 6BYF
- Type
- protein
- Length
- 1,473 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein phosphatase SIW14
- EC
- 3.1.3.48
- UniProt
- P53965
- Ligands
- CL
- Pockets
- 9 · best druggability 0.89
Structure
x-ray diffraction · 5 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Tyrosine-protein phosphatase SIW14 (EC 3.1.3.48) | protein | 165 | 47% helix, 13% strand | P53965 |
| B, E | Tyrosine-protein phosphatase SIW14 (EC 3.1.3.48) | protein | 164 | 46% helix, 13% strand | P53965 |
| C, H, I | Tyrosine-protein phosphatase SIW14 (EC 3.1.3.48) | protein | 163 | 47% helix, 13% strand | P53965 |
| F | Tyrosine-protein phosphatase SIW14 (EC 3.1.3.48) | protein | 162 | 48% helix, 14% strand | P53965 |
| G | Tyrosine-protein phosphatase SIW14 (EC 3.1.3.48) | protein | 164 | 47% helix, 12% strand | P53965 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains C, D, G
- CIT · Citric acid · additive · 9 copies · chains A, B, C, D, E, F, G, H, I
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, E, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1200 | 0.89 | 0.91 | 147 | empty |
| 2 | 588 | 0.65 | 0.76 | 75 | empty |
| 3 | 190 | 0.54 | 0.79 | 27 | empty |
| 4 | 185 | 0.48 | 0.76 | 30 | empty |
| 5 | 148 | 0.41 | 0.74 | 20 | empty |
Interfaces
19 interfaces between chains.
- C–D · 1333 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 1311 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 1249 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 581 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 578 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 modified (engineered).
Compared structures
- 6BYF · Crystal structure of the core catalytic domain of PP-IP phosphatase SIW14 from S.… · the same entry in another collection · chain H against H, TM-score 1.00
- P53965 · AlphaFold monomer V2.0 prediction for inositol phosphatase SIW14 (P53965) · a predicted model of the same protein · chain F against A, TM-score 0.99
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 P53965
- Elsewhere: RCSB PDB 6BYF · PDBe 6BYF · UniProt P53965
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