Research workbench
Crystal structure of human F508A NBD1 domain with ATP
Analyse Crystal structure of human F508A NBD1 domain with ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XMI
- Type
- protein
- Length
- 1,329 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystic fibrosis transmembrane conductance regulator
- EC
- 3.6.3.49
- UniProt
- P13569
- Ligands
- ATP, MG
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cystic fibrosis transmembrane conductance regulator (EC 3.6.3.49) | protein | 267 | 39% helix, 22% strand | P13569 |
| B | Cystic fibrosis transmembrane conductance regulator (EC 3.6.3.49) | protein | 258 | 42% helix, 21% strand | P13569 |
| C | Cystic fibrosis transmembrane conductance regulator (EC 3.6.3.49) | protein | 270 | 42% helix, 22% strand | P13569 |
| D | Cystic fibrosis transmembrane conductance regulator (EC 3.6.3.49) | protein | 268 | 40% helix, 22% strand | P13569 |
| E | Cystic fibrosis transmembrane conductance regulator (EC 3.6.3.49) | protein | 266 | 41% helix, 22% strand | P13569 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 5 copies · chains A, D, B, E, C
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 495 | 0.80 | 0.87 | 76 | MG, ATP |
| 2 | 583 | 0.78 | 0.84 | 68 | empty |
| 3 | 862 | 0.77 | 0.80 | 98 | MG, ATP |
| 4 | 793 | 0.73 | 0.78 | 74 | empty |
| 5 | 976 | 0.71 | 0.75 | 77 | empty |
Interfaces
7 interfaces between chains.
- A–D · 1279 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 1195 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 481 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 401 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 304 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1XMI · Crystal structure of human F508A NBD1 domain with ATP · the same entry in another collection · chain E against E, TM-score 1.00
- P13569 · AlphaFold monomer V2.0 prediction for cystic fibrosis transmembrane conductance regulator… · a predicted model of the same protein · chain A against A, TM-score 0.88
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 P13569
- Elsewhere: RCSB PDB 1XMI · PDBe 1XMI · UniProt P13569
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