MolNFT v1 · #31124 · protein
Crystal structure of tungstate complex of the phon protein from S. typhimurium
2AKC · Class a nonspecific acid phosphatase phon: “Crystal structure of tungstate complex of the phon protein from S. typhimurium”. X-ray diffraction, 1 ligand (WO4), 7 pockets (best druggability 0.74). MolNFT v1 #31124 on GenesisL1: 3D…
- 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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