MolNFT v1 · #150124 · protein
Human NBD1 of cftr in complex with nanobodies D12 and G3A
6GKD · Cystic fibrosis transmembrane conductance regulator: “Human NBD1 of cftr in complex with nanobodies D12 and G3A”. X-ray diffraction, 4 ligands (ATP, GLC, Z9N), 20 pockets (best druggability 0.86). MolNFT v1 #150124 on GenesisL1: 3D…
- PDB
- 6GKD
- Type
- protein
- Length
- 2,761 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystic fibrosis transmembrane conductance regulator; Nanobody D12; Nanobody G3A
- EC
- 3.6.3.49
- UniProt
- Q20BJ8
- Ligands
- ATP, GLC, Z9N, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 11 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cystic fibrosis transmembrane conductance regulator (EC 3.6.3.49) | protein | 216 | 33% helix, 28% strand | Q20BJ8 |
| B | Nanobody D12 | protein | 126 | 2% helix, 58% strand | — |
| C, H, Q, T | Nanobody G3A | protein | 123 | 7% helix, 54% strand | — |
| F | Cystic fibrosis transmembrane conductance regulator (EC 3.6.3.49) | protein | 209 | 34% helix, 27% strand | Q20BJ8 |
| G | Nanobody D12 | protein | 122 | 2% helix, 60% strand | — |
| I | Cystic fibrosis transmembrane conductance regulator (EC 3.6.3.49) | protein | 213 | 33% helix, 26% strand | Q20BJ8 |
| J, P, S | Nanobody D12 | protein | 123 | 2% helix, 62% strand | — |
| K | Nanobody G3A | protein | 121 | 7% helix, 50% strand | — |
| L, O, R | Cystic fibrosis transmembrane conductance regulator (EC 3.6.3.49) | protein | 215 | 33% helix, 27% strand | Q20BJ8 |
| M | Nanobody D12 | protein | 124 | 2% helix, 60% strand | — |
| N | Nanobody G3A | protein | 124 | 7% helix, 52% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 6 copies · chains A, O, Q, F, R, T, H, I, C, L, N, K
- GLC · alpha-D-glucopyranose · sugar · 5 copies · chains A, F, I, R, O
- Z9N · alpha-D-fructofuranose · sugar · 5 copies · chains A, L, F, I, R, O
- MG · Magnesium ion · metal · 10 copies · chains A, L, O, F, I, R
- GOL · Glycerol · additive · 2 copies · chains L, O, G, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 808 | 0.86 | 0.88 | 107 | ATP, MG |
| 2 | 1032 | 0.86 | 0.87 | 109 | ATP, MG |
| 3 | 718 | 0.85 | 0.89 | 97 | ATP |
| 4 | 1192 | 0.85 | 0.86 | 109 | ATP, MG |
| 5 | 1122 | 0.85 | 0.86 | 105 | ATP, MG |
Interfaces
49 interfaces between chains.
- I–J · 906 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 905 Ų buried · 11 hydrogen bonds · protein-protein
- F–G · 858 Ų buried · 11 hydrogen bonds · protein-protein
- O–P · 857 Ų buried · 13 hydrogen bonds · protein-protein
- L–M · 793 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6GKD · human NBD1 of CFTR in complex with nanobodies D12 and G3a · 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 6GKD · PDBe 6GKD · UniProt Q20BJ8
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