MolNFT v1 · #85861 · protein
Crystal structure of phosphoserine phosphatase from T.ONNURINEUS in complex with ndsb-201
4AP9: “Crystal structure of phosphoserine phosphatase from T.ONNURINEUS in complex with ndsb-201”. X-ray diffraction, 1 ligand (1PS), 17 pockets (best druggability 0.75). MolNFT v1 #85861 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4AP9
- Type
- protein
- Length
- 800 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoserine phosphatase
- EC
- 3.1.3.3
- UniProt
- B6YX36
- Ligands
- 1PS
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Phosphoserine phosphatase (EC 3.1.3.3) | protein | 200 | 42% helix, 24% strand | B6YX36 |
Ligands and binding sites
- 1PS · 3-pyridinium-1-ylpropane-1-sulfonate · ligand · 6 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 179 | 0.75 | 0.91 | 28 | empty |
| 2 | 583 | 0.70 | 0.79 | 60 | empty |
| 3 | 224 | 0.66 | 0.83 | 35 | 1PS |
| 4 | 162 | 0.65 | 0.86 | 22 | empty |
| 5 | 166 | 0.65 | 0.86 | 23 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1335 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1317 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 322 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 316 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 10 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 4AP9 · Crystal structure of phosphoserine phosphatase from T. onnurineus in complex with NDSB-201 · 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 B6YX36
- Elsewhere: RCSB PDB 4AP9 · PDBe 4AP9 · UniProt B6YX36
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