SMTL ID : 5kty.1

hMiro EF hand and cGTPase domains, GDP and Ca2+ bound state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

monomer

Ligands

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

GDP.1: 17 residues within 4Å: Chain A: V.250, N.252, C.253, G.254, K.255, S.256, G.257, L.267, K.271, K.352, D.354, L.355, T.382, C.383, N.384 Ligands: MG.2, GDP.3 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:V.250, A:N.252, A:C.253, A:G.254, A:K.255, A:S.256, A:G.257, A:K.271, A:K.271, A:K.352, A:K.352, A:T.382, A:T.382, A:C.383, A:N.384, A:N.384 Water bridges: A:K.278, A:K.278 Salt bridges: A:K.255, A:K.278, A:D.354 GDP.3: 11 residues within 4Å: Chain A: K.251, N.252, K.255, S.256, K.278, Y.280, D.299, S.301, E.302 Ligands: GDP.1, MG.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:V.250, A:K.251, A:N.252, A:E.302 Water bridges: A:K.278, A:K.278 Salt bridges: A:K.255, A:K.255, A:K.278

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: N.252 Ligands: GDP.1, GDP.3 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: D.21, D.23, D.25, T.27, E.32 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.21, A:D.25, A:T.27, A:E.32, H2O.2 CA.5: 5 residues within 4Å: Chain A: D.141, D.143, D.145, A.147, E.152 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.141, A:D.145, A:A.147, A:E.152, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Klosowiak, J.L. et al., Structural insights into Parkin substrate lysine targeting from minimal Miro substrates. Sci Rep (2016)

Release Date

2016-09-21

Peptides

Mitochondrial Rho GTPase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Mitochondrial Rho GTPase 1

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