SMTL ID : 5yhf.1

Crystal structure of SecDF in Super-membrane-facing form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

5 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.1: 12 residues within 4Å: Chain A: V.14, L.17, A.18, F.21, W.26, L.311, G.314, L.315, G.318, V.408, F.412 Ligands: OLC.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.14, A:A.18, A:F.21, A:F.21, A:L.311, A:L.311, A:L.315, A:F.412 Hydrogen bonds: A:W.26 OLC.2: 6 residues within 4Å: Chain A: T.371, M.375, L.382, V.411, F.412 Ligands: OLC.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.371, A:L.382, A:F.412 Hydrogen bonds: A:F.367, A:T.371 OLC.3: 8 residues within 4Å: Chain A: S.8, L.11, F.15, L.306, L.313, F.417, H.420, R.424 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.11, A:L.306, A:L.313, A:F.417 Salt bridges: A:H.420, A:R.424 OLC.4: 8 residues within 4Å: Chain A: L.35, S.309, L.313, L.323, L.331, T.334, L.335, A.338 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.313, A:L.323, A:L.331, A:T.334, A:L.335, A:L.335, A:A.338 OLC.5: 9 residues within 4Å: Chain A: A.321, T.322, I.379, L.382, L.383, A.385, A.386, V.401, A.404 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.379, A:L.382, A:L.382, A:L.383, A:A.386 Hydrogen bonds: A:T.322

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 5 residues within 4Å: Chain A: P.216, I.222, Q.226, A.227, V.228 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Furukawa, A. et al., Remote Coupled Drastic beta-Barrel to beta-Sheet Transition of the Protein Translocation Motor. Structure (2018)

Release Date

2018-02-14

Peptides

Protein translocase subunit SecDF: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Protein translocase subunit SecDF

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