SMTL ID : 5xap.1

Crystal structure of SecDF in I form (C2 space group)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

monomer

Ligands

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

OLC.1: 10 residues within 4Å: Chain A: P.6, A.9, L.12, L.13, L.16, L.302, F.306, I.309, F.416, W.419 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.9, A:L.12, A:L.13, A:F.306, A:I.309, A:F.416, A:W.419 OLC.2: 5 residues within 4Å: Chain A: F.289, A.290, G.293, P.434, W.436 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.289, A:A.290 OLC.3: 6 residues within 4Å: Chain A: F.442, D.443, F.444, P.447, V.680, Y.717 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.442, A:F.442, A:F.444, A:Y.717 Hydrogen bonds: A:D.443 Salt bridges: A:K.446 OLC.4: 2 residues within 4Å: Chain A: Y.388, N.389 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.388 OLC.5: 6 residues within 4Å: Chain A: Y.390, Y.575, L.578, L.579, G.582, V.586 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.575, A:L.578, A:L.579, A:V.586 OLC.6: 10 residues within 4Å: Chain A: L.14, T.15, G.18, S.19, Y.22, G.313, I.314, G.317, F.318, G.319 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.22, A:I.314, A:F.318 OLC.7: 10 residues within 4Å: Chain A: W.37, I.270, A.274, A.277, S.308, I.311, L.322, I.327, L.330, I.334 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.37, A:I.270, A:A.274, A:A.277, A:I.311, A:L.322, A:I.327, A:L.330, A:L.330, A:I.334

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

PEG.8: 3 residues within 4Å: Chain A: Y.291, W.436, S.673 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.672

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Furukawa, A. et al., Tunnel Formation Inferred from the I-Form Structures of the Proton-Driven Protein Secretion Motor SecDF. Cell Rep (2017)

Release Date

2017-05-17

Peptides

Protein translocase subunit SecD: 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 SecD

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