MolNFT v1 · #167385 · protein
Crystal structure of red kidney bean purple acid phosphatase in complex with adenosine 5'-(BETA,GAMMA IMIDO)TRIPHOSPHATE
6VJ7 · FE(3+)-ZN(2+) purple acid phosphatase: “Crystal structure of red kidney bean purple acid phosphatase in complex with adenosine 5'-(BETA,GAMMA…”. X-ray diffraction, 8 ligands (ANP, NAG, BMA), 20 pockets (best druggability 0.67).…
- PDB
- 6VJ7
- Type
- protein
- Length
- 1,698 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FE(3+)-ZN(2+) purple acid phosphatase
- EC
- 3.1.3.2
- UniProt
- P80366
- Ligands
- ANP, NAG, BMA, FUC, ZN, FE, NA, SO4
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FE(3+)-ZN(2+) purple acid phosphatase (EC 3.1.3.2) | protein | 424 | 17% helix, 30% strand | P80366 |
| B | FE(3+)-ZN(2+) purple acid phosphatase (EC 3.1.3.2) | protein | 425 | 17% helix, 29% strand | P80366 |
| C | FE(3+)-ZN(2+) purple acid phosphatase (EC 3.1.3.2) | protein | 423 | 17% helix, 29% strand | P80366 |
| D | FE(3+)-ZN(2+) purple acid phosphatase (EC 3.1.3.2) | protein | 426 | 18% helix, 29% strand | P80366 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 3 copies · chains A, D, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 23 copies · chains A, B, D, C
- BMA · beta-D-mannopyranose · sugar · 6 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 24 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 31 copies · chains A, B, C, D
- GOL · Glycerol · additive · 9 copies · chains A, D, B, C
- PGE · Triethylene glycol · additive · 7 copies · chains B, D, C, A
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, D
- IPA · Isopropyl alcohol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.67 | 0.79 | 41 | GOL, PG4, SO4, PGE |
| 2 | 452 | 0.67 | 0.79 | 41 | EDO, GOL |
| 3 | 384 | 0.64 | 0.78 | 32 | EDO |
| 4 | 400 | 0.64 | 0.78 | 32 | empty |
| 5 | 65 | 0.49 | 0.85 | 17 | EDO |
Interfaces
4 interfaces between chains.
- A–D · 1533 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1495 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 505 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 474 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 glycan, 2 disulfide, 1 covalent (N-glycosylation, disulfide, additive adduct).
Compared structures
- 6VJ7 · Crystal structure of red kidney bean purple acid phosphatase in complex with adenosine… · the same entry in another collection · chain D against D, TM-score 1.00
- P80366 · AlphaFold monomer V2.0 prediction for FE(3+)-ZN(2+) purple acid phosphatase (P80366) · a predicted model of the same protein · chain C 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 P80366
- Elsewhere: RCSB PDB 6VJ7 · PDBe 6VJ7 · UniProt P80366
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