SMTL ID : 3bs6.1 (2 other biounits)

1.8 Angstrom crystal structure of the periplasmic domain of the membrane insertase YidC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

5 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: Y.175, E.176 Ligands: CA.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.175, A:E.176, H2O.3, H2O.14 CA.2: 2 residues within 4Å: Chain A: E.176 Ligands: CA.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.176, A:E.176, H2O.145 CA.3: 1 residues within 4Å: Chain A: E.173 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.173, A:E.173 CA.4: 1 residues within 4Å: Chain A: N.70 No protein-ligand interaction detected (PLIP) CA.5: 1 residues within 4Å: Chain A: A.69 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.69, H2O.30, H2O.38

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.6: 5 residues within 4Å: Chain A: F.138, Q.140, N.218, Y.220, K.234 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

2 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

3 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

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Inner membrane protein oxaA

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