SMTL ID : 5yew.2 (1 other biounit)

Structural basis for GTP hydrolysis and conformational change of mitofusin 1 in mediating mitochondrial fusion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-dimer

Ligands

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

GDP.1: 21 residues within 4Å: Chain A: S.85, S.86, G.87, K.88, S.89, S.90, P.102, S.103, G.104, I.105, T.109, N.237, R.238, D.240, S.284, A.285, K.286 Chain B: E.245 Ligands: BEF.2, K.3, MG.4 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.85, A:S.86, A:G.87, A:G.87, A:K.88, A:S.89, A:S.90, A:S.90, A:G.104, A:N.237, A:R.238, A:S.284, A:A.285, A:K.286, B:E.245, B:E.245 Salt bridges: A:K.88, A:D.240 GDP.5: 21 residues within 4Å: Chain A: E.245 Chain B: S.85, S.86, G.87, K.88, S.89, S.90, P.102, S.103, G.104, I.105, T.109, N.237, R.238, D.240, S.284, A.285, K.286 Ligands: BEF.6, K.7, MG.8 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.85, B:S.86, B:G.87, B:G.87, B:K.88, B:S.89, B:S.90, B:S.90, B:G.104, B:N.237, B:R.238, B:S.284, B:A.285, B:K.286, A:E.245, A:E.245 Salt bridges: B:K.88, B:D.240

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

BEF.2: 12 residues within 4Å: Chain A: R.83, T.84, K.88, G.106, H.107, I.108, T.109, P.180, G.181 Ligands: GDP.1, K.3, MG.4 No protein-ligand interaction detected (PLIP) BEF.6: 12 residues within 4Å: Chain B: R.83, T.84, K.88, G.106, H.107, I.108, T.109, P.180, G.181 Ligands: GDP.5, K.7, MG.8 No protein-ligand interaction detected (PLIP)

2 x K: POTASSIUM ION(Non-covalent)

K.3: 5 residues within 4Å: Chain A: S.85, G.104, G.106 Ligands: GDP.1, BEF.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:G.104, A:G.106 K.7: 5 residues within 4Å: Chain B: S.85, G.104, G.106 Ligands: GDP.5, BEF.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:G.104, B:G.106

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: S.89, T.109, D.178 Ligands: GDP.1, BEF.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.89, A:T.109 MG.8: 5 residues within 4Å: Chain B: S.89, T.109, D.178 Ligands: GDP.5, BEF.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.89, B:T.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, L. et al., Structural basis for GTP hydrolysis and conformational change of MFN1 in mediating membrane fusion. Nat. Struct. Mol. Biol. (2018)

Release Date

2018-01-31

Peptides

Mitofusin-1,Mitofusin-1 fusion protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
C

Mitofusin-1,Mitofusin-1 fusion protein

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