Research workbench
Structure of NBD1 from murine cftr- F508S mutant
Analyse Structure of NBD1 from murine cftr- F508S mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XF9
- Type
- protein
- Length
- 1,054 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystic fibrosis transmembrane conductance regulator
- UniProt
- P26361
- Ligands
- ATP, MG
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cystic fibrosis transmembrane conductance regulator | protein | 264 | 42% helix, 23% strand | P26361 |
| B | Cystic fibrosis transmembrane conductance regulator | protein | 265 | 42% helix, 23% strand | P26361 |
| C | Cystic fibrosis transmembrane conductance regulator | protein | 265 | 42% helix, 23% strand | P26361 |
| D | Cystic fibrosis transmembrane conductance regulator | protein | 260 | 42% helix, 23% strand | P26361 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D
- ACY · Acetic acid · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 727 | 0.71 | 0.78 | 69 | MG |
| 2 | 326 | 0.62 | 0.79 | 45 | MG, ATP |
| 3 | 335 | 0.59 | 0.77 | 37 | empty |
| 4 | 210 | 0.54 | 0.78 | 41 | MG, ATP |
| 5 | 208 | 0.52 | 0.77 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 737 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 666 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 332 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1XF9 · Structure of NBD1 from murine CFTR- F508S mutant · the same entry in another collection · chain D against D, TM-score 1.00
- P26361 · AlphaFold monomer V2.0 prediction for cystic fibrosis transmembrane conductance regulator… · a predicted model of the same protein · chain D against A, TM-score 0.93
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 P26361
- Elsewhere: RCSB PDB 1XF9 · PDBe 1XF9 · UniProt P26361
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