Research workbench
Human NBD1 of CFTR in complex with nanobodies D12 and T8
Analyse Human NBD1 of CFTR in complex with nanobodies D12 and T8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GK4
- Type
- protein
- Length
- 894 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.91
- Source
- Homo sapiens; Lama glama
- Molecule
- Cystic fibrosis transmembrane conductance regulator; Nanobody D12; Nanobody T8
- EC
- 3.6.3.49
- UniProt
- Q20BJ8
- Ligands
- ATP, MG
- Pockets
- 14 · best druggability 0.70
Structure
x-ray diffraction · resolution 2.91 · 6 distinct chains · 18% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cystic fibrosis transmembrane conductance regulator (EC 3.6.3.49) | protein | 210 | 33% helix, 26% strand | Q20BJ8 |
| B | Nanobody D12 | protein | 121 | 2% helix, 56% strand | — |
| C | Nanobody T8 | protein | 114 | 5% helix, 54% strand | — |
| D | Cystic fibrosis transmembrane conductance regulator (EC 3.6.3.49) | protein | 211 | 34% helix, 27% strand | Q20BJ8 |
| E | Nanobody D12 | protein | 122 | 5% helix, 58% strand | — |
| F | Nanobody T8 | protein | 116 | 5% helix, 55% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, D
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.70 | 0.92 | 30 | empty |
| 2 | 310 | 0.68 | 0.83 | 44 | MG |
| 3 | 52 | 0.64 | 0.95 | 24 | empty |
| 4 | 274 | 0.60 | 0.79 | 35 | ATP, MG |
| 5 | 213 | 0.57 | 0.79 | 27 | empty |
Interfaces
5 interfaces between chains.
- D–F · 920 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 865 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 811 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 791 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 163 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6GK4 · Human NBD1 of cftr in complex with nanobodies D12 and T8 · 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 Q20BJ8
- Elsewhere: RCSB PDB 6GK4 · PDBe 6GK4 · UniProt Q20BJ8
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