MolNFT v1 · #172382 · protein
Crystal structure of the 5-phosphatase domain of SYNAPTOJANIN1 in complex with a nanobody
7A0V · Synaptojanin-1: “Crystal structure of the 5-phosphatase domain of SYNAPTOJANIN1 in complex with a nanobody”. X-ray diffraction, 2 ligands (MG, PO4), 16 pockets (best druggability 0.81). MolNFT v1 #172382 on GenesisL1: 3D structure…
- PDB
- 7A0V
- Type
- protein
- Length
- 1,331 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Synaptojanin-1; Nanobody 13015
- EC
- 3.1.3.36
- UniProt
- O43426
- Ligands
- MG, PO4
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Synaptojanin-1 (EC 3.1.3.36) | protein | 333 | 26% helix, 32% strand | O43426 |
| B | Nanobody 13015 | protein | 123 | 7% helix, 41% strand | — |
| C | Synaptojanin-1 (EC 3.1.3.36) | protein | 309 | 27% helix, 32% strand | O43426 |
| D | Nanobody 13015 | protein | 125 | 10% helix, 46% strand | — |
| E | Synaptojanin-1 (EC 3.1.3.36) | protein | 317 | 24% helix, 32% strand | O43426 |
| F | Nanobody 13015 | protein | 124 | 10% helix, 45% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, C, E
- PO4 · Phosphate ion · ion · 3 copies · chains A, F, E
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.81 | 0.83 | 103 | PO4 |
| 2 | 406 | 0.80 | 0.89 | 37 | empty |
| 3 | 124 | 0.64 | 0.87 | 25 | empty |
| 4 | 154 | 0.62 | 0.85 | 28 | empty |
| 5 | 348 | 0.61 | 0.78 | 57 | GOL |
Interfaces
11 interfaces between chains.
- A–C · 750 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 612 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 591 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 563 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 435 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7A0V · Crystal structure of the 5-phosphatase domain of Synaptojanin1 in complex with a nanobody · 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 7A0V · PDBe 7A0V · UniProt O43426
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