MolNFT v1 · #186205 · protein
Crystal structure of prevotella sp. CAG:617 multiple inositol polyphosphate phosphatase, complex with myo-inositol hexakissulfate
7R5Y · Histidine acid phosphatase: “Crystal structure of prevotella sp. CAG:617 multiple inositol polyphosphate phosphatase, complex with…”. X-ray diffraction, 2 ligands (IHS, SO4), 20 pockets (best druggability 0.70). MolNFT v1 #186205 on…
- PDB
- 7R5Y
- Type
- protein
- Length
- 2,465 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidine acid phosphatase
- UniProt
- R7PD89
- Ligands
- IHS, SO4
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histidine acid phosphatase | protein | 409 | 53% helix, 13% strand | R7PD89 |
| B | Histidine acid phosphatase | protein | 407 | 53% helix, 13% strand | R7PD89 |
| C | Histidine acid phosphatase | protein | 408 | 53% helix, 13% strand | R7PD89 |
| D | Histidine acid phosphatase | protein | 413 | 52% helix, 13% strand | R7PD89 |
| E, F | Histidine acid phosphatase | protein | 414 | 51% helix, 14% strand | R7PD89 |
Ligands and binding sites
- IHS · D-myo-inositol-hexasulphate · ligand · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 811 | 0.70 | 0.76 | 89 | empty |
| 2 | 404 | 0.64 | 0.78 | 47 | IHS |
| 3 | 470 | 0.63 | 0.76 | 32 | empty |
| 4 | 409 | 0.62 | 0.77 | 47 | IHS |
| 5 | 394 | 0.62 | 0.77 | 44 | IHS |
Interfaces
9 interfaces between chains.
- C–D · 1052 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 1038 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 509 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 384 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 370 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7R5Y · Crystal Structure of Prevotella sp. CAG:617 Multiple Inositol Polyphosphate Phosphatase… · 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 R7PD89
- Elsewhere: RCSB PDB 7R5Y · PDBe 7R5Y · UniProt R7PD89
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