Research workbench

Human NBD1 of cftr in complex with nanobodies D12 and G3A

Analyse Human NBD1 of cftr in complex with nanobodies D12 and G3A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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.

Pocket	Volume (Å³)	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 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 905 Å² buried · 11 hydrogen bonds · protein-protein
F–G · 858 Å² buried · 11 hydrogen bonds · protein-protein
O–P · 857 Å² buried · 13 hydrogen bonds · protein-protein
L–M · 793 Å² 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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