Research workbench
Structure of francisella tularensis acid phosphatase a (acpa) bound to orthovanadate
Analyse Structure of francisella tularensis acid phosphatase a (acpa) bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D1G
- Type
- protein
- Length
- 953 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acid phosphatase
- EC
- 3.1.3.2
- UniProt
- Q2A5P7
- Ligands
- ETE, ETX, DVT, VO4, UNX
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acid phosphatase (EC 3.1.3.2) | protein | 481 | 27% helix, 16% strand | Q2A5P7 |
| B | Acid phosphatase (EC 3.1.3.2) | protein | 472 | 26% helix, 16% strand | Q2A5P7 |
Ligands and binding sites
- ETE · 2-{2-[2-2-(methoxy-ethoxy)-ethoxy]-ethoxy}-ethanol · ligand · chains A
- ETX · 2-ethoxyethanol · ligand · chains A
- DVT · Decavanadate · ligand · chains B
- VO4 · Vanadate ion · ion · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.73 | 0.92 | 36 | empty |
| 2 | 275 | 0.55 | 0.77 | 35 | empty |
| 3 | 175 | 0.47 | 0.76 | 26 | empty |
| 4 | 171 | 0.47 | 0.76 | 27 | empty |
| 5 | 134 | 0.37 | 0.73 | 31 | VO4 |
Interfaces
1 interface between chains.
- A–B · 1293 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2D1G · Structure of Francisella tularensis Acid Phosphatase A (AcpA) bound to orthovanadate · 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 Q2A5P7
- Elsewhere: RCSB PDB 2D1G · PDBe 2D1G · UniProt Q2A5P7
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