SMTL ID : 6q3q.1

Arabidopsis OM64 TPR domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x GLY- SER- LYS- MET- GLU- GLU- VAL- ASP: GLY-SER-LYS-MET-GLU-GLU-VAL-ASP(Non-covalent)

GLY-SER-LYS-MET-GLU-GLU-VAL-ASP.1: 17 residues within 4Å: Chain A: K.10, N.14, Y.17, Y.29, T.41, N.45, A.48, V.74, K.75, L.78, R.79, T.82, E.104, N.107, T.109 Chain B: K.115 Ligands: GOL.10 21 PLIP interactions: 19 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:N.14, A:T.41, A:A.48 Hydrogen bonds: A:N.14, A:Y.17, A:N.45, A:N.45, A:N.45, A:K.75, A:R.79, A:E.104, A:N.107 Water bridges: A:K.20, A:N.45, A:K.75, A:E.104, A:T.109, B:K.115 Salt bridges: A:K.10, A:K.75, B:K.115 GLY-SER-LYS-MET-GLU-GLU-VAL-ASP.2: 17 residues within 4Å: Chain A: K.115 Chain B: K.10, N.14, Y.17, Y.29, T.41, N.45, A.48, V.74, K.75, L.78, R.79, T.82, E.104, N.107, T.109 Ligands: GOL.4 23 PLIP interactions: 21 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:N.14, B:T.41, B:A.48 Hydrogen bonds: B:N.14, B:Y.17, B:N.45, B:N.45, B:N.45, B:K.75, B:R.79, B:E.104, B:N.107 Water bridges: B:K.10, B:N.45, B:K.75, B:K.75, B:E.104, B:T.109, B:T.109, A:K.115 Salt bridges: B:K.10, B:K.75, A:K.115

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: C.54, C.55, F.56, Q.57, Q.58 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.55, A:F.56, A:Q.57, A:Q.58 GOL.4: 5 residues within 4Å: Chain A: R.116, K.119 Chain B: E.52, T.82 Ligands: GLY-SER-LYS-MET-GLU-GLU-VAL-ASP.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.119, A:K.119 Water bridges: A:K.115 GOL.5: 4 residues within 4Å: Chain A: Y.90, K.91, H.120 Ligands: SO4.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.91 Water bridges: A:H.120, A:I.121, A:I.121 GOL.9: 5 residues within 4Å: Chain B: C.54, C.55, F.56, Q.57, Q.58 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:C.55, B:F.56, B:Q.57, B:Q.58, B:Q.58 GOL.10: 5 residues within 4Å: Chain A: E.52, T.82 Chain B: R.116, K.119 Ligands: GLY-SER-LYS-MET-GLU-GLU-VAL-ASP.1 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.119, B:K.119 Water bridges: B:K.115, B:R.116, B:R.118 GOL.11: 4 residues within 4Å: Chain B: G.1, N.2, M.3, E.4 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.1, B:G.1, B:M.3, B:E.4, B:E.4 Water bridges: B:M.3 GOL.12: 4 residues within 4Å: Chain B: T.30, I.33, Y.43, R.46 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.46, B:R.46

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 5 residues within 4Å: Chain A: R.89, Y.90, K.91, E.92 Ligands: GOL.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.90, A:K.91, A:E.92 Water bridges: A:R.89, A:K.91 Salt bridges: A:R.89, A:K.91 SO4.7: 5 residues within 4Å: Chain A: E.7, K.10, N.39, T.41, Y.42 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.39, A:N.39 Water bridges: A:T.41, A:T.41 Salt bridges: A:K.10 SO4.8: 4 residues within 4Å: Chain A: Q.21, W.22, N.23, L.53 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:W.22, A:N.23, A:N.23 Water bridges: A:K.20, A:K.20, A:W.22, A:K.24 SO4.13: 4 residues within 4Å: Chain B: R.89, Y.90, K.91, E.92 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.90, B:K.91, B:E.92 Water bridges: B:V.88, B:R.89 SO4.14: 5 residues within 4Å: Chain B: E.7, K.10, N.39, T.41, Y.42 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.39, B:N.39, B:T.41 Water bridges: B:E.7, B:E.7, B:E.7 Salt bridges: B:K.10 SO4.15: 5 residues within 4Å: Chain B: K.20, Q.21, W.22, N.23, K.24 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.21, B:W.22, B:N.23, B:N.23, B:K.24 Salt bridges: B:K.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nickel, C. et al., Phosphorylation of the outer membrane mitochondrial protein OM64 influences protein import into mitochondria. Mitochondrion (2019)

Release Date

2018-12-19

Peptides

Outer envelope protein 64, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Outer envelope protein 64, mitochondrial