MolNFT v1 · #75802 · protein
Crystal structure of raph complexed with SPO0F
3Q15 · Response regulator aspartate phosphatase H: “Crystal structure of raph complexed with SPO0F”. X-ray diffraction, 2 ligands (MG, SO4), 8 pockets (best druggability 0.70). MolNFT v1 #75802 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3Q15
- Type
- protein
- Length
- 913 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Response regulator aspartate phosphatase H; Sporulation initiation phosphotransferase F
- EC
- 3.1.-.-, 2.7.-.-
- UniProt
- Q59HN8, P06628
- Ligands
- MG, SO4
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 73% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Response regulator aspartate phosphatase H (EC 3.1.-.-) | protein | 365 | 81% helix, 1% strand | Q59HN8 |
| B | Response regulator aspartate phosphatase H (EC 3.1.-.-) | protein | 332 | 80% helix, 0% strand | Q59HN8 |
| C | Sporulation initiation phosphotransferase F (EC 2.7.-.-) | protein | 116 | 47% helix, 20% strand | P06628 |
| D | Sporulation initiation phosphotransferase F (EC 2.7.-.-) | protein | 100 | 45% helix, 22% strand | P06628 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.70 | 0.79 | 47 | empty |
| 2 | 558 | 0.64 | 0.75 | 41 | empty |
| 3 | 525 | 0.62 | 0.75 | 52 | empty |
| 4 | 309 | 0.57 | 0.76 | 41 | SO4 |
| 5 | 170 | 0.49 | 0.77 | 33 | MG |
Interfaces
3 interfaces between chains.
- A–C · 1107 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 1008 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 633 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3Q15 · Crystal Structure of RapH complexed with Spo0F · the same entry in another collection · chain D against D, TM-score 1.00
- P06628 · AlphaFold monomer V2.0 prediction for sporulation initiation phosphotransferase F (P06628) · a predicted model of the same protein · chain C against A, TM-score 0.97
- Q59HN8 · AlphaFold monomer V2.0 prediction for response regulator aspartate phosphatase H (Q59HN8) · a predicted model of the same protein · chain B against A, TM-score 0.83
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 Q59HN8
- Every structure of UniProt P06628
- Elsewhere: RCSB PDB 3Q15 · PDBe 3Q15 · UniProt Q59HN8 · UniProt P06628
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.