SMTL ID : 6gkd.1

human NBD1 of CFTR in complex with nanobodies D12 and G3a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.99 Å

Oligo State

hetero-6-6-6-mer

Ligands

5 x GLC- Z9N: alpha-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-Z9N.1: 10 residues within 4Å: Chain A: Y.98, R.99, V.103, V.145, D.148, Y.152, L.177, K.181 Chain J: G.56, E.57 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain J Hydrogen bonds: A:R.99, A:R.99, A:V.145, A:Y.152, J:E.57 GLC-Z9N.2: 9 residues within 4Å: Chain D: Y.98, R.99, V.145, D.148, Y.152, L.177, K.181 Chain G: G.56, E.57 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain G Hydrogen bonds: D:R.99, D:V.145, D:D.148, D:K.181, G:G.56 GLC-Z9N.3: 12 residues within 4Å: Chain G: Y.98, R.99, V.103, V.145, Y.146, K.147, D.148, Y.152, L.177, M.178 Chain P: G.56, E.57 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain P Hydrogen bonds: G:R.99, G:R.99, G:Y.146, P:E.57 GLC-Z9N.4: 11 residues within 4Å: Chain A: G.56, E.57 Chain M: Y.98, R.99, S.102, V.103, V.145, Y.152, L.177, M.178, K.181 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:R.99, M:V.145, M:S.102 GLC-Z9N.5: 11 residues within 4Å: Chain D: G.56, E.57 Chain P: Y.98, R.99, V.145, Y.146, D.148, Y.152, L.177, M.178, K.181 3 PLIP interactions: 2 interactions with chain P, 1 interactions with chain D Hydrogen bonds: P:V.145, P:Y.146, P:M.178, P:Y.98, P:Y.98, D:E.57

6 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.6: 14 residues within 4Å: Chain A: W.16, V.23, T.43, G.44, A.45, G.46, K.47, T.48, S.49, Q.76 Chain M: Y.98 Chain O: R.57, R.58 Ligands: MG.7 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain O Hydrogen bonds: A:T.43, A:G.44, A:A.45, A:G.46, A:K.47, A:T.48, A:S.49, A:S.49, A:Q.76, A:Q.76, O:R.57, O:R.58 Water bridges: A:T.48 Salt bridges: A:K.47, A:K.47, O:R.58 pi-Stacking: A:W.16, A:W.16, A:W.16 ATP.9: 14 residues within 4Å: Chain D: W.16, V.23, T.43, G.44, A.45, G.46, K.47, T.48, S.49, Q.76 Chain P: Y.98 Chain R: R.57, R.58 Ligands: MG.10 13 PLIP interactions: 10 interactions with chain D, 3 interactions with chain R Hydrogen bonds: D:G.44, D:G.46, D:K.47, D:T.48, D:S.49, R:R.57, R:R.58, R:R.58 Salt bridges: D:K.47, D:K.47 pi-Stacking: D:W.16, D:W.16, D:W.16 ATP.13: 14 residues within 4Å: Chain D: Y.98 Chain F: R.57, R.58 Chain G: W.16, V.23, T.43, G.44, A.45, G.46, K.47, T.48, S.49, Q.76 Ligands: MG.14 14 PLIP interactions: 12 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:G.44, G:G.46, G:K.47, G:T.48, G:S.49, G:S.49, G:Q.76, F:R.58 Salt bridges: G:K.47, G:K.47 pi-Stacking: G:W.16, G:W.16, G:W.16 pi-Cation interactions: F:R.57 ATP.15: 15 residues within 4Å: Chain A: Y.98 Chain C: R.57, D.59 Chain J: W.16, V.23, T.43, G.44, A.45, G.46, K.47, T.48, S.49, M.52, Q.76 Ligands: MG.16 17 PLIP interactions: 16 interactions with chain J, 1 interactions with chain C Hydrogen bonds: J:G.44, J:A.45, J:G.46, J:K.47, J:T.48, J:S.49, J:S.49, J:Q.76 Water bridges: J:K.47, J:T.48, J:D.155 Salt bridges: J:K.47, J:K.47 pi-Stacking: J:W.16, J:W.16, J:W.16 pi-Cation interactions: C:R.57 ATP.17: 15 residues within 4Å: Chain J: Y.98 Chain L: R.57, R.58 Chain M: W.16, V.23, S.42, T.43, G.44, A.45, G.46, K.47, T.48, S.49, Q.76 Ligands: MG.18 21 PLIP interactions: 17 interactions with chain M, 4 interactions with chain L Hydrogen bonds: M:S.42, M:T.43, M:G.44, M:A.45, M:G.46, M:K.47, M:T.48, M:S.49, M:S.49, M:Q.76, L:R.57, L:R.58 Water bridges: M:K.47, M:K.47, L:R.58, L:R.58 Salt bridges: M:K.47, M:K.47 pi-Stacking: M:W.16, M:W.16, M:W.16 ATP.21: 15 residues within 4Å: Chain G: Y.98 Chain I: R.57, R.58, D.59 Chain P: W.16, V.23, T.43, G.44, A.45, G.46, K.47, T.48, S.49, Q.76 Ligands: MG.22 15 PLIP interactions: 13 interactions with chain P, 2 interactions with chain I Hydrogen bonds: P:G.44, P:A.45, P:G.46, P:K.47, P:T.48, P:T.48, P:S.49, P:S.49, I:R.58 Salt bridges: P:K.47, P:K.47, I:R.58 pi-Stacking: P:W.16, P:W.16, P:W.16

10 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 4 residues within 4Å: Chain A: T.48, Q.76, D.155 Ligands: ATP.6 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.48, H2O.1 MG.8: 3 residues within 4Å: Chain A: E.87 Chain J: E.87 Chain M: E.87 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain D: T.48, Q.76, D.155 Ligands: ATP.9 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:T.48, H2O.2 MG.11: 3 residues within 4Å: Chain D: E.87 Chain G: E.87 Chain P: E.87 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain D: F.91 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain G: T.48, Q.76 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.48 MG.16: 4 residues within 4Å: Chain J: T.48, Q.76, D.155 Ligands: ATP.15 3 PLIP interactions: 1 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:T.48, H2O.5, H2O.5 MG.18: 4 residues within 4Å: Chain M: T.48, Q.76, D.155 Ligands: ATP.17 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:T.48 MG.19: 1 residues within 4Å: Chain M: G.92 No protein-ligand interaction detected (PLIP) MG.22: 4 residues within 4Å: Chain P: T.48, Q.76, D.155 Ligands: ATP.21 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:T.48

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.20: 4 residues within 4Å: Chain J: R.99, L.177 Chain M: G.56, E.57 3 PLIP interactions: 1 interactions with chain M, 2 interactions with chain J Hydrogen bonds: M:E.57, J:R.99, J:L.177 GOL.23: 3 residues within 4Å: Chain E: R.71, D.72 Chain R: R.19 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain R Hydrogen bonds: E:D.72, R:R.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sigoillot, M. et al., Domain-interface dynamics of CFTR revealed by stabilizing nanobodies. Nat Commun (2019)

Release Date

2019-06-19

Peptides

Cystic fibrosis transmembrane conductance regulator: ADGJMP
Nanobody D12: BEHKNQ
Nanobody G3a: CFILOR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
F

G
I

J
L

M
O

P
R

B
B

E
G

H
J

K
M

N
P

Q
S

C
C

F
H

I
K

L
N

O
Q

R
T

Cystic fibrosis transmembrane conductance regulator

Nanobody D12

Nanobody G3a

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