Research workbench
Red kidney bean purple acid phosphatase in complex with adenosine divanadate
Analyse Red kidney bean purple acid phosphatase in complex with adenosine divanadate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HWR
- Type
- protein
- Length
- 1,698 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.95
- Source
- Phaseolus vulgaris
- Molecule
- Fe(3+)-Zn(2+) purple acid phosphatase
- EC
- 3.1.3.2
- UniProt
- P80366
- Ligands
- H1T, VV6, H1Q, H1W, VN3, NAG, FUC, NA, ZN, FE, SO4
- Pockets
- 18 · best druggability 0.69
Structure
x-ray diffraction · resolution 1.95 · 4 distinct chains · 18% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Fe(3+)-Zn(2+) purple acid phosphatase (EC 3.1.3.2) | protein | 423 | 18% helix, 30% strand | P80366 |
| B | Fe(3+)-Zn(2+) purple acid phosphatase (EC 3.1.3.2) | protein | 425 | 18% helix, 29% strand | P80366 |
| A | Fe(3+)-Zn(2+) purple acid phosphatase (EC 3.1.3.2) | protein | 424 | 17% helix, 30% strand | P80366 |
| D | Fe(3+)-Zn(2+) purple acid phosphatase (EC 3.1.3.2) | protein | 426 | 18% helix, 30% strand | P80366 |
Ligands and binding sites
- H1T · [[[[bis($l^{1}-oxidanyl)-[$l^{1}-oxidanyl-[tris($l^{1}-oxidanyl)vanadiooxy]vanadio]oxy-vanadio]oxy-bis($l^{1}-oxidanyl)vanadio]oxy-oxidanylidene-vanadio]-[bis($l^{1}-oxidanyl)vanadio]-$l^{3}-oxidanyl]-tetrakis($l^{1}-oxidanyl)vanadium · ligand · chains C, D
- VV6 · [[[[bis(oxidanyl)-[tris(oxidanyl) vanadiooxy]vanadio]oxy-bis(oxidanyl)vanadio]-oxidanylidene-vanadio]oxy-oxidanyl-vanadio]oxy-tetrakis(oxidanyl)vanadium · ligand · chains B, A
- H1Q · adenosine divanadate · ligand · chains B, A
- H1W · pentakis(oxidanyl)vanadium · ligand · chains D
- VN3 · Vanadate ion · ligand · chains D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains C, B, A, D
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains D
- NA · Sodium ion · metal · 5 copies · chains C, D, B, A
- ZN · Zinc ion · metal · 4 copies · chains C, B, A, D
- FE · Fe (III) ion · metal · 4 copies · chains C, B, A, D
- SO4 · Sulfate ion · ion · 42 copies · chains C, B, A, D
- EDO · 1,2-ethanediol · additive · 12 copies · chains C, D, B, A
- GOL · Glycerol · additive · 5 copies · chains C, D, B, A
- PGE · Triethylene glycol · additive · 3 copies · chains C, A, B, D
- IPA · Isopropyl alcohol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 435 | 0.69 | 0.80 | 39 | GOL, EDO, SO4 |
| 2 | 444 | 0.68 | 0.80 | 42 | SO4, GOL |
| 3 | 403 | 0.64 | 0.78 | 32 | empty |
| 4 | 414 | 0.63 | 0.77 | 35 | empty |
| 5 | 212 | 0.47 | 0.74 | 29 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1486 Ų buried · 8 hydrogen bonds · protein-protein
- B–A · 1480 Ų buried · 9 hydrogen bonds · protein-protein
- C–A · 476 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 475 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 6HWR · Red kidney bean purple acid phosphatase in complex with adenosine divanadate · 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 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 P80366
- Elsewhere: RCSB PDB 6HWR · PDBe 6HWR · UniProt P80366
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