SMTL ID : 5dv5.1

The fatty acid-responsive FadR repressor of Vibrio alginolyticus complex with Palmitoyl-CoA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

4 x PKZ: Palmitoyl-CoA(Non-covalent)

PKZ.1: 27 residues within 4Å: Chain A: L.122, L.123, A.124, A.125, R.126, T.127, I.129, N.203, D.206, I.225, L.229, Y.233, V.236, G.237, Y.240, F.241, R.274, G.277, M.278, S.280, A.281, W.284 Chain B: R.135, Y.136, K.139, S.217, R.266 26 PLIP interactions: 22 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.122, A:L.123, A:A.125, A:R.126, A:I.129, A:I.225, A:Y.233, A:Y.233, A:V.236, A:Y.240, A:F.241 Hydrogen bonds: A:R.126, A:R.126, A:S.280, B:Y.136, B:S.217 Water bridges: A:A.124, A:A.124, A:R.274, A:Y.276, A:S.280 Salt bridges: A:R.274, A:R.274, A:R.274, B:R.135, B:R.266 PKZ.2: 37 residues within 4Å: Chain A: I.103, L.104, L.107, R.147, N.151, S.155, Y.174, K.177, V.178, F.204, Y.205, M.208, Q.211, R.212, F.215, H.216, Q.220, I.221, L.224, I.225, N.227, G.228, L.229 Chain B: I.41, W.42, G.44, P.48, W.81, F.95, M.96, I.103, T.106, L.107, L.110, I.118, L.229 Ligands: PKZ.4 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.103, A:L.224, A:L.229, B:F.95, B:I.103 Hydrogen bonds: A:R.147, A:N.151, A:S.155, A:S.155, A:Y.205, A:R.212, A:N.227 Water bridges: A:Q.211 Salt bridges: A:K.177, A:R.212, A:H.216 pi-Stacking: A:Y.174, A:Y.174 PKZ.3: 27 residues within 4Å: Chain A: R.135, Y.136, K.139, R.266 Chain B: L.122, L.123, A.124, A.125, R.126, T.127, I.129, N.203, D.206, I.225, F.226, L.229, Y.233, V.236, G.237, Y.240, F.241, R.274, G.277, M.278, S.280, A.281, W.284 29 PLIP interactions: 23 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:L.123, B:R.126, B:I.129, B:I.225, B:F.226, B:F.226, B:L.229, B:Y.233, B:Y.233, B:V.236, B:V.236, B:Y.240, B:F.241 Hydrogen bonds: B:R.126, B:R.126, B:T.127, B:S.280, A:R.135, A:R.135, A:Y.136, A:A.140, A:R.266 Water bridges: B:A.124, B:A.124, B:S.280 Salt bridges: B:R.274, B:R.274, B:R.274 pi-Cation interactions: A:R.266 PKZ.4: 35 residues within 4Å: Chain A: I.41, W.42, P.48, W.81, F.95, M.96, I.103, T.106, L.107, L.110, I.118, L.229 Chain B: L.104, L.107, R.147, N.151, S.155, Y.174, K.177, V.178, F.204, Y.205, M.208, Q.211, R.212, F.215, H.216, Q.220, I.221, L.224, I.225, N.227, G.228, L.229 Ligands: PKZ.2 24 PLIP interactions: 19 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.104, B:L.107, B:F.215, B:F.215, B:F.215, B:I.221, A:W.42, A:W.42, A:W.81, A:I.103, A:L.107 Hydrogen bonds: B:N.151, B:N.151, B:S.155, B:R.212, B:N.227 Water bridges: B:T.148 Salt bridges: B:R.147, B:R.147, B:K.177, B:R.212, B:H.216 pi-Stacking: B:Y.174, B:Y.174

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feng, Y.J. et al., Snapshort of Vibrio FadR-ligand complex structure reveals a new mechanism for bacterial fatty acid sensing. To Be Published

Release Date

2016-10-05

Peptides

GntR family transcriptional regulator: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GntR family transcriptional regulator

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