Research workbench
Crystal structure of the neurofibromin SEC14-pH module containing the patient derived mutation I1584V
Analyse Crystal structure of the neurofibromin SEC14-pH module containing the patient… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P7Z
- Type
- protein
- Length
- 540 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neurofibromin
- UniProt
- P21359
- Ligands
- PEV, POP, NA
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neurofibromin | protein | 270 | 30% helix, 30% strand | P21359 |
Ligands and binding sites
- PEV · (1S)-2-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate · ligand · 2 copies · chains A, B
- POP · Pyrophosphate 2- · ligand · 2 copies · chains B
- NA · Sodium ion · metal · chains A
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 | 614 | 0.86 | 0.90 | 38 | PEV |
| 2 | 605 | 0.85 | 0.89 | 38 | PEV |
| 3 | 625 | 0.72 | 0.79 | 74 | empty |
| 4 | 247 | 0.55 | 0.78 | 38 | empty |
| 5 | 100 | 0.48 | 0.81 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 611 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3P7Z · Crystal structure of the Neurofibromin Sec14-PH module containing the patient derived… · 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 P21359
- Elsewhere: RCSB PDB 3P7Z · PDBe 3P7Z · UniProt P21359
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