SMTL ID : 3t34.1

Arabidopsis thaliana dynamin-related protein 1A (AtDRP1A) in prefission state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-dimer

Ligands

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

GDP.1: 22 residues within 4Å: Chain A: S.44, S.45, G.46, K.47, S.48, S.49, R.62, G.63, K.212, D.214, L.215, V.240, V.241, N.242, R.243, S.244, Q.245, I.248 Chain B: D.217 Ligands: ALF.2, MG.3, NA.4 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.42, A:S.44, A:S.45, A:G.46, A:K.47, A:S.48, A:S.49, A:S.49, A:G.63, A:G.63, A:K.212, A:K.212, A:N.242 Water bridges: A:T.68, A:T.68, A:G.145 Salt bridges: A:K.47, A:D.214, B:D.217 pi-Cation interactions: A:K.212 GDP.5: 24 residues within 4Å: Chain A: D.217 Chain B: S.44, S.45, G.46, K.47, S.48, S.49, R.62, G.63, S.64, V.67, K.212, D.214, L.215, V.240, V.241, N.242, R.243, S.244, Q.245, I.248 Ligands: ALF.6, MG.7, NA.8 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.44, B:S.45, B:G.46, B:K.47, B:S.48, B:S.49, B:G.63, B:S.64, B:K.212, B:K.212, B:N.242, B:N.242 Water bridges: B:P.61, B:T.68 Salt bridges: B:K.47, B:D.214, A:D.217

2 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.2: 12 residues within 4Å: Chain A: Q.43, S.44, K.47, G.65, I.66, V.67, T.68, L.143, G.145 Ligands: GDP.1, MG.3, NA.4 No protein-ligand interaction detected (PLIP) ALF.6: 13 residues within 4Å: Chain B: G.42, Q.43, S.44, K.47, G.65, I.66, V.67, T.68, L.143, G.145 Ligands: GDP.5, MG.7, NA.8 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: S.48, T.68 Ligands: GDP.1, ALF.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.48, A:T.68, H2O.2, H2O.2 MG.7: 7 residues within 4Å: Chain B: K.47, S.48, T.68, D.142, L.143 Ligands: GDP.5, ALF.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.48, B:T.68, H2O.9, H2O.9

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 7 residues within 4Å: Chain A: S.44, G.63, S.64, G.65, V.67 Ligands: GDP.1, ALF.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.63, A:V.67 NA.8: 7 residues within 4Å: Chain B: S.44, G.63, S.64, G.65, V.67 Ligands: GDP.5, ALF.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.44, B:V.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, L.M. et al., Structural basis for mechanochemical role of Arabidopsis thaliana dynamin-related protein in membrane fission. J Mol Cell Biol (2011)

Release Date

2012-06-06

Peptides

Dynamin-related protein 1A, LINKER, Dynamin-related protein 1A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dynamin-related protein 1A, LINKER, Dynamin-related protein 1A

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