Research workbench
Crystal structure of tungstate complex of the phon protein from S. typhimurium
Analyse Crystal structure of tungstate complex of the phon protein from S. typhimurium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AKC
- Type
- protein
- Length
- 875 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Class a nonspecific acid phosphatase phon
- EC
- 3.1.3.2
- Ligands
- WO4
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 70% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Class a nonspecific acid phosphatase phon (EC 3.1.3.2) | protein | 218 | 70% helix, 1% strand | — |
| B, C, D | Class a nonspecific acid phosphatase phon (EC 3.1.3.2) | protein | 219 | 69% helix, 1% strand | — |
Ligands and binding sites
- WO4 · Tungstate(vi)ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 634 | 0.74 | 0.81 | 61 | empty |
| 2 | 598 | 0.72 | 0.79 | 59 | empty |
| 3 | 381 | 0.58 | 0.76 | 42 | empty |
| 4 | 122 | 0.50 | 0.80 | 24 | WO4 |
| 5 | 128 | 0.45 | 0.77 | 24 | WO4 |
Interfaces
3 interfaces between chains.
- A–B · 1735 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1714 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 228 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2AKC · Crystal structure of tungstate complex of the PhoN protein from S. typhimurium · 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
- Elsewhere: RCSB PDB 2AKC · PDBe 2AKC
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