SMTL ID : 1xmi.2 (1 other biounit)

Crystal structure of human F508A NBD1 domain with ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-10-mer

Ligands

10 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.78, Q.106, D.185 Ligands: ATP.2 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.78, H2O.5, H2O.6 MG.3: 4 residues within 4Å: Chain B: T.78, Q.106, D.185 Ligands: ATP.4 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.78, H2O.10, H2O.12 MG.5: 3 residues within 4Å: Chain C: T.78, Q.106 Ligands: ATP.6 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.78, H2O.17, H2O.17 MG.7: 3 residues within 4Å: Chain D: T.78, Q.106 Ligands: ATP.8 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:T.78, H2O.23, H2O.23 MG.9: 3 residues within 4Å: Chain E: T.78, Q.106 Ligands: ATP.10 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:T.78, H2O.28, H2O.29 MG.11: 3 residues within 4Å: Chain F: T.78, Q.106 Ligands: ATP.12 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:T.78, H2O.34, H2O.34 MG.13: 4 residues within 4Å: Chain G: T.78, Q.106, D.185 Ligands: ATP.14 3 PLIP interactions: 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:T.78, H2O.40, H2O.40 MG.15: 4 residues within 4Å: Chain H: T.78, Q.106, D.185 Ligands: ATP.16 3 PLIP interactions: 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:T.78, H2O.44, H2O.44 MG.17: 4 residues within 4Å: Chain I: T.78, Q.106, D.185 Ligands: ATP.18 3 PLIP interactions: 1 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:T.78, H2O.50, H2O.50 MG.19: 4 residues within 4Å: Chain J: T.78, Q.106, D.185 Ligands: ATP.20 3 PLIP interactions: 1 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:T.78, H2O.54, H2O.55

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

ATP.2: 13 residues within 4Å: Chain A: W.14, V.53, S.72, T.73, G.74, A.75, G.76, K.77, T.78, S.79, Q.106 Chain I: F.263 Ligands: MG.1 21 PLIP interactions: 18 interactions with chain A, 3 interactions with chain I Hydrogen bonds: A:T.73, A:G.74, A:A.75, A:G.76, A:K.77, A:T.78, A:T.78, A:S.79, A:S.79, A:Q.106 Water bridges: A:K.77, A:T.78, A:D.185, I:D.264 Salt bridges: A:K.77, A:K.77 pi-Stacking: A:W.14, A:W.14, A:W.14, I:F.263, I:F.263 ATP.4: 13 residues within 4Å: Chain B: W.14, V.53, S.72, T.73, G.74, A.75, G.76, K.77, T.78, S.79, Q.106 Chain G: F.263 Ligands: MG.3 20 PLIP interactions: 17 interactions with chain B, 3 interactions with chain G Hydrogen bonds: B:G.74, B:A.75, B:G.76, B:K.77, B:T.78, B:T.78, B:S.79, B:S.79, B:Q.106 Water bridges: B:K.77, B:T.78, B:D.185, G:D.264 Salt bridges: B:K.77, B:K.77 pi-Stacking: B:W.14, B:W.14, B:W.14, G:F.263, G:F.263 ATP.6: 13 residues within 4Å: Chain C: W.14, V.53, S.72, T.73, G.74, A.75, G.76, K.77, T.78, S.79, Q.106 Chain D: F.263 Ligands: MG.5 18 PLIP interactions: 16 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:T.73, C:G.74, C:A.75, C:G.76, C:K.77, C:T.78, C:T.78, C:S.79, C:S.79, C:Q.106 Water bridges: C:K.77 Salt bridges: C:K.77, C:K.77 pi-Stacking: C:W.14, C:W.14, C:W.14, D:F.263, D:F.263 ATP.8: 14 residues within 4Å: Chain B: F.263, D.264 Chain D: W.14, V.53, S.72, T.73, G.74, A.75, G.76, K.77, T.78, S.79, Q.106 Ligands: MG.7 22 PLIP interactions: 19 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:T.73, D:G.74, D:A.75, D:G.76, D:K.77, D:T.78, D:T.78, D:S.79, D:S.79, D:Q.106, B:D.264 Water bridges: D:K.77, D:T.78, D:Q.106, D:D.261 Salt bridges: D:K.77, D:K.77 pi-Stacking: D:W.14, D:W.14, D:W.14, B:F.263, B:F.263 ATP.10: 13 residues within 4Å: Chain E: W.14, V.53, S.72, T.73, G.74, A.75, G.76, K.77, T.78, S.79, Q.106 Chain F: F.263 Ligands: MG.9 18 PLIP interactions: 2 interactions with chain F, 16 interactions with chain E pi-Stacking: F:F.263, F:F.263, E:W.14, E:W.14, E:W.14 Hydrogen bonds: E:G.74, E:A.75, E:G.76, E:K.77, E:T.78, E:S.79, E:S.79, E:Q.106 Water bridges: E:K.77, E:T.78, E:T.78 Salt bridges: E:K.77, E:K.77 ATP.12: 14 residues within 4Å: Chain A: F.263, D.264 Chain F: W.14, V.53, S.72, T.73, G.74, A.75, G.76, K.77, T.78, S.79, Q.106 Ligands: MG.11 21 PLIP interactions: 17 interactions with chain F, 4 interactions with chain A Hydrogen bonds: F:G.74, F:A.75, F:G.76, F:K.77, F:T.78, F:T.78, F:S.79, F:S.79, F:Q.106, A:D.264 Water bridges: F:K.77, F:T.78, F:Q.106, A:D.264 Salt bridges: F:K.77, F:K.77 pi-Stacking: F:W.14, F:W.14, F:W.14, A:F.263, A:F.263 ATP.14: 14 residues within 4Å: Chain G: W.14, V.53, S.72, T.73, G.74, A.75, G.76, K.77, T.78, S.79, Q.106 Chain H: F.263, D.264 Ligands: MG.13 20 PLIP interactions: 17 interactions with chain G, 3 interactions with chain H Hydrogen bonds: G:G.74, G:A.75, G:G.76, G:K.77, G:T.78, G:T.78, G:S.79, G:S.79, G:Q.106, H:D.264 Water bridges: G:K.77, G:T.78, G:Q.106 Salt bridges: G:K.77, G:K.77 pi-Stacking: G:W.14, G:W.14, G:W.14, H:F.263, H:F.263 ATP.16: 14 residues within 4Å: Chain C: F.263, D.264 Chain H: W.14, V.53, S.72, T.73, G.74, A.75, G.76, K.77, T.78, S.79, Q.106 Ligands: MG.15 22 PLIP interactions: 18 interactions with chain H, 4 interactions with chain C Hydrogen bonds: H:G.74, H:A.75, H:G.76, H:G.76, H:K.77, H:T.78, H:T.78, H:S.79, H:S.79, H:Q.106, H:Q.106, C:D.264, C:D.264 Water bridges: H:K.77, H:T.78, H:Q.106 Salt bridges: H:K.77, H:K.77 pi-Stacking: H:W.14, H:W.14, C:F.263, C:F.263 ATP.18: 14 residues within 4Å: Chain I: W.14, V.53, S.72, T.73, G.74, A.75, G.76, K.77, T.78, S.79, Q.106 Chain J: F.263, D.264 Ligands: MG.17 21 PLIP interactions: 3 interactions with chain J, 18 interactions with chain I Hydrogen bonds: J:D.264, I:T.73, I:G.74, I:A.75, I:G.76, I:K.77, I:T.78, I:T.78, I:S.79, I:S.79, I:Q.106 pi-Stacking: J:F.263, J:F.263, I:W.14, I:W.14, I:W.14 Water bridges: I:K.77, I:T.78, I:Q.106 Salt bridges: I:K.77, I:K.77 ATP.20: 14 residues within 4Å: Chain E: F.263, D.264 Chain J: W.14, V.53, S.72, T.73, G.74, A.75, G.76, K.77, T.78, S.79, Q.106 Ligands: MG.19 21 PLIP interactions: 3 interactions with chain E, 18 interactions with chain J Hydrogen bonds: E:D.264, J:T.73, J:G.74, J:A.75, J:G.76, J:G.76, J:K.77, J:T.78, J:T.78, J:S.79, J:S.79, J:Q.106 pi-Stacking: E:F.263, E:F.263, J:W.14, J:W.14 Water bridges: J:K.77, J:T.78, J:Q.106 Salt bridges: J:K.77, J:K.77

Links

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Citation

Lewis, H.A. et al., Impact of the delta-F508 Mutation in First Nucleotide-binding Domain of Human Cystic Fibrosis Transmembrane Conductance Regulator on Domain Folding and Structure. J.Biol.Chem. (2005)

Release Date

2004-11-09

Peptides

Cystic fibrosis transmembrane conductance regulator: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
C

C
A

D
D

E
A

F
D

G
B

H
E

I
B

J
E

Cystic fibrosis transmembrane conductance regulator

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