SMTL ID : 2x2f.1

Dynamin 1 GTPase dimer, short axis form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

GDP.1: 22 residues within 4Å: Chain A: S.41, A.42, G.43, K.44, S.45, S.46, R.59, G.60, S.61, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Chain B: D.211 Ligands: ALF.2, MG.3, NA.4 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.41, A:A.42, A:G.43, A:K.44, A:S.45, A:S.46, A:G.60, A:S.61, A:K.206, A:K.206, A:N.236, A:Q.239 Water bridges: A:S.45, A:S.46, A:T.65, A:N.236, A:R.237, A:S.238 Salt bridges: A:K.44, A:D.208, B:D.211 GDP.5: 22 residues within 4Å: Chain A: D.211 Chain B: S.41, A.42, G.43, K.44, S.45, S.46, R.59, G.60, S.61, K.206, D.208, L.209, V.235, N.236, R.237, S.238, Q.239, I.242 Ligands: ALF.6, MG.7, NA.8 22 PLIP interactions: 19 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.41, B:A.42, B:G.43, B:K.44, B:S.45, B:S.46, B:S.46, B:G.60, B:K.206, B:K.206, B:N.236, B:Q.239 Water bridges: B:P.58, B:T.65, B:D.208, B:N.236, B:S.238, A:D.211, A:D.211 Salt bridges: B:K.44, B:D.208, A:D.211

2 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.2: 13 residues within 4Å: Chain A: Q.40, S.41, K.44, S.45, G.62, I.63, V.64, T.65, P.138, G.139 Ligands: GDP.1, MG.3, NA.4 No protein-ligand interaction detected (PLIP) ALF.6: 13 residues within 4Å: Chain B: Q.40, S.41, K.44, S.45, G.62, I.63, V.64, T.65, P.138, G.139 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.45, T.65 Ligands: GDP.1, ALF.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.45, A:T.65, H2O.3, H2O.7 MG.7: 5 residues within 4Å: Chain B: S.45, T.65, D.136 Ligands: GDP.5, ALF.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.45, B:T.65, H2O.9, H2O.13

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

NA.4: 7 residues within 4Å: Chain A: S.41, G.60, S.61, G.62, V.64 Ligands: GDP.1, ALF.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.41, A:V.64 NA.8: 7 residues within 4Å: Chain B: S.41, G.60, S.61, G.62, V.64 Ligands: GDP.5, ALF.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.41, B:S.61, B:V.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chappie, J.S. et al., G Domain Dimerization Controls Dynamin'S Assembly-Stimulated Gtpase Activity. Nature (2010)

Release Date

2010-04-28

Peptides

DYNAMIN-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

DYNAMIN-1

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