MolNFT v1 · #172394 · protein
Crystal structure of the 5-phosphatase domain of SYNAPTOJANIN1 bound to its substrate DIC8-PI(3,4,5)P3 in complex with a nanobody
7A17 · Isoform 2 of synaptojanin-1: “Crystal structure of the 5-phosphatase domain of SYNAPTOJANIN1 bound to its substrate DIC8-PI(3,4,5)P3 in…”. X-ray diffraction, 3 ligands (IP9, MG, PO4), 17 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 7A17
- Type
- protein
- Length
- 1,335 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 2 of synaptojanin-1; Nanobody 13015
- EC
- 3.1.3.36
- UniProt
- O43426
- Ligands
- IP9, MG, PO4
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 21% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform 2 of synaptojanin-1 (EC 3.1.3.36) | protein | 336 | 27% helix, 34% strand | O43426 |
| B | Nanobody 13015 | protein | 119 | 10% helix, 43% strand | — |
| C | Isoform 2 of synaptojanin-1 (EC 3.1.3.36) | protein | 319 | 26% helix, 32% strand | O43426 |
| D | Nanobody 13015 | protein | 123 | 10% helix, 47% strand | — |
| E | Isoform 2 of synaptojanin-1 (EC 3.1.3.36) | protein | 313 | 23% helix, 34% strand | O43426 |
| F | Nanobody 13015 | protein | 125 | 10% helix, 46% strand | — |
Ligands and binding sites
- IP9 · (2R)-3-{[(R)-{[(1S,2S,3R,4S,5S,6S)-2,6-dihydroxy-3,4,5-tris(phosphonooxy)cyclohexyl]oxy}(hydroxy) phosphoryl]oxy}propane -1,2-diyl dioctanoate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, C
- PO4 · Phosphate ion · ion · 4 copies · chains C, E
- GOL · Glycerol · additive · 2 copies · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 824 | 0.83 | 0.85 | 106 | GOL |
| 2 | 406 | 0.82 | 0.90 | 37 | empty |
| 3 | 150 | 0.70 | 0.90 | 27 | empty |
| 4 | 140 | 0.70 | 0.90 | 25 | empty |
| 5 | 163 | 0.63 | 0.85 | 27 | empty |
Interfaces
11 interfaces between chains.
- A–C · 872 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 583 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 553 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 553 Ų buried · 7 hydrogen bonds · protein-protein
- C–F · 433 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7A17 · Crystal structure of the 5-phosphatase domain of Synaptojanin1 bound to its substrate… · the same entry in another collection · chain F against F, TM-score 1.00
- O43426 · AlphaFold monomer V2.0 prediction for synaptojanin-1 (O43426) · a predicted model of the same protein · chain E against A, TM-score 0.98
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 O43426
- Elsewhere: RCSB PDB 7A17 · PDBe 7A17 · UniProt O43426
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