- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.80 Å
- Oligo State
- homo-tetramer
- Ligands
- 10 x CA: CALCIUM ION(Non-covalent)
- 2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
PG4.6: 6 residues within 4Å:- Chain A: F.138, Q.140, N.218, Y.220, K.234
- Ligands: 2PE.23
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:N.190
- Water bridges: A:Q.140, A:Q.140, A:K.234, A:K.234
PG4.17: 6 residues within 4Å:- Chain B: F.138, Q.140, N.218, Y.220, K.234
- Ligands: 2PE.29
6 PLIP interactions:6 interactions with chain B- Hydrogen bonds: B:N.190
- Water bridges: B:T.60, B:Q.140, B:Q.140, B:K.234, B:K.234
- 6 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
PGE.7: 8 residues within 4Å:- Chain A: H.212, N.213, T.245, G.246, A.247, M.248, N.249
- Ligands: EDO.10
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:A.247, A:N.249
PGE.8: 5 residues within 4Å:- Chain A: E.91, Q.93, V.111, N.122, N.249
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:E.91, A:N.122, A:N.249
- Water bridges: A:Q.93
PGE.18: 8 residues within 4Å:- Chain B: H.212, N.213, T.245, G.246, A.247, M.248, N.249
- Ligands: EDO.21
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:A.247, B:N.249
PGE.19: 5 residues within 4Å:- Chain B: E.91, Q.93, V.111, N.122, N.249
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:E.91, B:N.122, B:N.249
- Water bridges: B:Q.93
PGE.24: 6 residues within 4Å:- Chain C: N.77, V.78, E.79, Y.83, P.95, T.97
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:E.79, C:E.79, C:Y.83, C:Y.83
- Water bridges: C:T.97
PGE.30: 6 residues within 4Å:- Chain D: N.77, V.78, E.79, Y.83, P.95, T.97
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:E.79, D:Y.83
- 14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.9: 1 residues within 4Å:- Chain A: K.9
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:K.9
EDO.10: 8 residues within 4Å:- Chain A: S.137, P.211, H.212, N.213, S.235, M.248, N.249
- Ligands: PGE.7
7 PLIP interactions:7 interactions with chain A- Hydrogen bonds: A:S.137, A:H.212, A:N.213, A:N.249
- Water bridges: A:S.137, A:N.213, A:S.235
EDO.11: 2 residues within 4Å:- Chain A: Q.259, D.260
1 PLIP interactions:1 interactions with chain A- Water bridges: A:D.260
EDO.20: 1 residues within 4Å:- Chain B: K.9
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:K.9
EDO.21: 8 residues within 4Å:- Chain B: S.137, P.211, H.212, N.213, S.235, M.248, N.249
- Ligands: PGE.18
7 PLIP interactions:7 interactions with chain B- Hydrogen bonds: B:S.137, B:H.212, B:N.213, B:N.249
- Water bridges: B:S.137, B:N.213, B:S.235
EDO.22: 2 residues within 4Å:- Chain B: Q.259, D.260
1 PLIP interactions:1 interactions with chain B- Water bridges: B:D.260
EDO.25: 3 residues within 4Å:- Chain C: Y.32, Y.204, P.256
No protein-ligand interaction detected (PLIP)EDO.26: 3 residues within 4Å:- Chain C: S.7, K.9, V.84
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:S.7, C:S.7
- Water bridges: C:K.9
EDO.27: 3 residues within 4Å:- Chain C: L.5, S.7, D.81
1 PLIP interactions:1 interactions with chain C- Water bridges: C:T.16
EDO.28: 2 residues within 4Å:- Chain C: A.31, Y.32
No protein-ligand interaction detected (PLIP)EDO.31: 3 residues within 4Å:- Chain D: Y.32, Y.204, P.256
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:Y.32
EDO.32: 3 residues within 4Å:- Chain D: S.7, K.9, V.84
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:S.7, D:S.7
- Water bridges: D:K.9
EDO.33: 3 residues within 4Å:- Chain D: L.5, S.7, D.81
1 PLIP interactions:1 interactions with chain D- Water bridges: D:T.16
EDO.34: 2 residues within 4Å:- Chain D: A.31, Y.32
No protein-ligand interaction detected (PLIP)- 2 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)
2PE.23: 14 residues within 4Å:- Chain C: R.20, Q.56, R.73, F.138, Q.140, N.190, T.216, N.218, Y.220, K.234, S.235, Q.236, P.237
- Ligands: PG4.6
7 PLIP interactions:7 interactions with chain C- Hydrogen bonds: C:R.20, C:R.73, C:K.234
- Water bridges: C:Q.140, C:Q.140, C:Q.140, C:N.190
2PE.29: 14 residues within 4Å:- Chain D: R.20, Q.56, R.73, F.138, Q.140, N.190, T.216, N.218, Y.220, K.234, S.235, Q.236, P.237
- Ligands: PG4.17
7 PLIP interactions:7 interactions with chain D- Hydrogen bonds: D:R.20, D:R.73, D:K.234
- Water bridges: D:Q.140, D:Q.140, D:Q.140, D:N.190
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Ravaud, S. et al., The Crystal Structure of the Periplasmic Domain of the Escherichia coli Membrane Protein Insertase YidC Contains a Substrate Binding Cleft. J.Biol.Chem. (2008)
- Release Date
- 2008-02-12
- Peptides
- Inner membrane protein oxaA: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
BD
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.80 Å
- Oligo State
- homo-tetramer
- Ligands
- 10 x CA: CALCIUM ION(Non-covalent)
- 2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
- 6 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
- 14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 2 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Ravaud, S. et al., The Crystal Structure of the Periplasmic Domain of the Escherichia coli Membrane Protein Insertase YidC Contains a Substrate Binding Cleft. J.Biol.Chem. (2008)
- Release Date
- 2008-02-12
- Peptides
- Inner membrane protein oxaA: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
BD
B