Research workbench
Crystal structure of the sec-pH domain of the human neurofibromatosis type 1 protein
Analyse Crystal structure of the sec-pH domain of the human neurofibromatosis type 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D4Q
- Type
- protein
- Length
- 512 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neurofibromin
- UniProt
- P21359
- Ligands
- OXN, POP
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neurofibromin | protein | 257 | 32% helix, 32% strand | P21359 |
| B | Neurofibromin | protein | 255 | 34% helix, 31% strand | P21359 |
Ligands and binding sites
- OXN · Oxtoxynol-10 · ligand · 2 copies · chains A, B
- POP · Pyrophosphate 2- · ligand · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 563 | 0.86 | 0.90 | 38 | OXN |
| 2 | 489 | 0.86 | 0.91 | 37 | OXN |
| 3 | 1061 | 0.75 | 0.78 | 131 | empty |
| 4 | 111 | 0.58 | 0.85 | 23 | empty |
| 5 | 58 | 0.35 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 545 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2D4Q · Crystal structure of the Sec-PH domain of the human neurofibromatosis type 1 protein · 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 2D4Q · PDBe 2D4Q · UniProt P21359
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