SMTL ID : 6jtg.1

Structural insights into G domain dimerization and pathogenic mutations of OPA1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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

GDP.1: 22 residues within 4Å: Chain A: D.34, S.36, A.37, G.38, K.39, T.40, S.41, R.54, G.55, S.56, K.206, D.208, L.209, V.239, V.240, T.241, G.242, K.243, G.244 Ligands: MG.2, BEF.3, K.4 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:D.34, A:S.36, A:G.38, A:K.39, A:T.40, A:S.41, A:S.41, A:G.55, A:S.56, A:K.206, A:K.206, A:T.241, A:T.241, A:G.242 Water bridges: A:S.56, A:S.56, A:G.244, A:G.244, A:N.245 Salt bridges: A:K.39, A:D.208 GDP.5: 22 residues within 4Å: Chain B: D.34, S.36, A.37, G.38, K.39, T.40, S.41, R.54, G.55, S.56, K.206, D.208, L.209, V.239, V.240, T.241, G.242, K.243, G.244 Ligands: MG.6, BEF.7, K.8 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:D.34, B:S.36, B:G.38, B:K.39, B:T.40, B:S.41, B:S.41, B:G.55, B:S.56, B:K.206, B:K.206, B:T.241, B:G.242 Water bridges: B:S.56, B:S.56, B:G.244, B:G.244, B:N.245 Salt bridges: B:K.39, B:D.208

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: T.40, T.61, D.136 Ligands: GDP.1, BEF.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.40, A:T.61 MG.6: 5 residues within 4Å: Chain B: T.40, T.61, D.136 Ligands: GDP.5, BEF.7 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.40, B:T.61

2 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.3: 12 residues within 4Å: Chain A: Q.35, S.36, K.39, T.40, E.58, M.59, M.60, T.61, G.139 Ligands: GDP.1, MG.2, K.4 No protein-ligand interaction detected (PLIP) BEF.7: 12 residues within 4Å: Chain B: Q.35, S.36, K.39, T.40, E.58, M.59, M.60, T.61, G.139 Ligands: GDP.5, MG.6, K.8 No protein-ligand interaction detected (PLIP)

2 x K: POTASSIUM ION(Non-covalent)

K.4: 5 residues within 4Å: Chain A: S.36, G.55, E.58 Ligands: GDP.1, BEF.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.36, A:G.55, A:E.58 K.8: 5 residues within 4Å: Chain B: S.36, G.55, E.58 Ligands: GDP.5, BEF.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:S.36, B:G.55, B:E.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, C. et al., Structural insights into G domain dimerization and pathogenic mutation of OPA1. J.Cell Biol. (2020)

Release Date

2020-04-22

Peptides

Dynamin-like 120 kDa protein, mitochondrial,OPA1 protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Dynamin-like 120 kDa protein, mitochondrial,OPA1 protein