MolNFT v1 · #31855 · protein
Crystal structure of apha class B acid PHOSPHATASE/PHOSPHOTRANSFERASE ternary complex with adenosine and phosphate at 2 a resolution
2B8J: “Crystal structure of apha class B acid PHOSPHATASE/PHOSPHOTRANSFERASE ternary complex with adenosine and…”. X-ray diffraction, 6 ligands (SPM, ADN, MG), 4 pockets (best druggability 0.63). MolNFT v1 #31855 on GenesisL1: 3D…
- PDB
- 2B8J
- Type
- protein
- Length
- 422 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Class B acid phosphatase
- EC
- 3.1.3.2
- UniProt
- P32697
- Ligands
- SPM, ADN, MG, AU, AU3, PO4
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Class B acid phosphatase (EC 3.1.3.2) | protein | 211 | 36% helix, 17% strand | P32697 |
Ligands and binding sites
- SPM · Spermine · ligand · chains A
- ADN · Adenosine · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- AU · Gold ion · metal · chains A
- AU3 · Gold 3+ ion · metal
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 240 | 0.63 | 0.82 | 34 | MG, SPM, PO4, AU |
| 2 | 282 | 0.61 | 0.80 | 42 | MG, ADN |
| 3 | 64 | 0.33 | 0.76 | 17 | empty |
| 4 | 59 | 0.32 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1441 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2B8J · Crystal structure of AphA class B acid phosphatase/phosphotransferase ternary complex… · 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 P32697
- Elsewhere: RCSB PDB 2B8J · PDBe 2B8J · UniProt P32697
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