SMTL ID : 6b9f.1

Human ATL1 mutant - F151S bound to GDPAlF4-

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: L.107, T.108, G.109, F.110, S.111, W.112 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.109, A:W.112, A:W.112 Water bridges: A:G.109 GOL.2: 6 residues within 4Å: Chain A: L.88, R.89, Y.92, T.108, G.109, W.126 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.108 Water bridges: A:R.89 GOL.3: 10 residues within 4Å: Chain A: E.372, Q.431, Y.432, H.435 Chain B: N.368, E.372, L.428, Q.431, Y.432, H.435 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.372, A:Q.431, B:N.368, B:Q.431, B:Y.432 GOL.4: 4 residues within 4Å: Chain A: N.263, S.265, W.303, S.309 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.265, A:S.265 GOL.8: 6 residues within 4Å: Chain B: Q.36, S.111, E.119, T.120, T.121, Q.124 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.36, B:E.119, B:T.121, B:Q.124 Water bridges: B:S.111, B:Q.124, B:Q.124 GOL.9: 7 residues within 4Å: Chain B: L.107, T.108, G.109, F.110, S.111, W.112 Ligands: GOL.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.109, B:W.112, B:W.112 GOL.10: 4 residues within 4Å: Chain B: W.112, F.282, D.283 Ligands: GOL.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.112, B:P.280 Water bridges: B:W.112 GOL.11: 6 residues within 4Å: Chain B: L.88, R.89, Y.92, T.108, G.109, W.126 4 PLIP interactions: 4 interactions with chain B Water bridges: B:A.32, B:R.89, B:G.109, B:G.109

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 5 residues within 4Å: Chain A: S.81, T.120, D.146 Ligands: GDP.6, ALF.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.81, A:T.120, H2O.3, H2O.3 MG.12: 4 residues within 4Å: Chain B: S.81, T.120 Ligands: GDP.13, ALF.14 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.81, B:T.120, H2O.14, H2O.15

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.6: 19 residues within 4Å: Chain A: R.77, K.78, G.79, K.80, S.81, F.82, W.112, R.113, G.114, R.217, D.218, H.271, P.272, V.276, A.277, F.282, F.293 Ligands: MG.5, ALF.7 21 PLIP interactions: 18 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.77, A:K.78, A:G.79, A:K.80, A:S.81, A:F.82, A:R.113, A:R.113, A:R.217, A:H.271 Water bridges: A:S.111, A:T.120, A:T.120, B:Q.180, B:S.220, B:S.220 Salt bridges: A:R.77, A:R.77, A:K.80, A:D.218 pi-Cation interactions: A:H.271 GDP.13: 18 residues within 4Å: Chain B: R.77, K.78, G.79, K.80, S.81, F.82, W.112, R.113, G.114, R.217, D.218, H.271, P.272, V.276, F.282, F.293 Ligands: MG.12, ALF.14 23 PLIP interactions: 21 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.77, B:K.78, B:G.79, B:K.80, B:S.81, B:F.82, B:R.113, B:R.113, B:T.120, B:R.217, B:H.271 Water bridges: B:R.77, B:S.81, B:G.114, B:D.218, A:Q.180, A:S.220 Salt bridges: B:R.77, B:R.77, B:K.80, B:D.218 pi-Stacking: B:F.82 pi-Cation interactions: B:H.271

2 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.7: 10 residues within 4Å: Chain A: F.76, R.77, K.80, R.118, E.119, T.120, T.147, G.149 Ligands: MG.5, GDP.6 No protein-ligand interaction detected (PLIP) ALF.14: 10 residues within 4Å: Chain B: F.76, R.77, K.80, R.118, E.119, T.120, T.147, G.149 Ligands: MG.12, GDP.13 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

O'Donnell, J.P. et al., A hereditary spastic paraplegia-associated atlastin variant exhibits defective allosteric coupling in the catalytic core. J. Biol. Chem. (2018)

Release Date

2017-12-06

Peptides

Atlastin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Atlastin-1