SMTL ID : 3d71.1

Crystal structure of E253Q BMRR bound to 22 base pair promoter site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 1 residues within 4Å: Chain B: H.189 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.189 ZN.12: 1 residues within 4Å: Chain D: H.189 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.189

2 x FLC: CITRATE ANION(Non-covalent)

FLC.2: 9 residues within 4Å: Chain B: P.144, V.147, Y.187, F.224, Q.253, I.255, Y.268 Ligands: IMD.7, IMD.8 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:V.147 Hydrogen bonds: B:Y.187, B:Q.253 Water bridges: B:N.149 Salt bridges: D:K.2 FLC.13: 9 residues within 4Å: Chain D: P.144, V.147, Y.187, F.224, Q.253, I.255, Y.268 Ligands: IMD.18, IMD.19 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:V.147 Hydrogen bonds: D:Q.253 Water bridges: D:N.149 Salt bridges: B:K.2

6 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.3: 4 residues within 4Å: Chain B: R.111, R.133, V.194, N.197 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.111, B:R.133, B:V.194 Water bridges: B:R.111 PGO.4: 4 residues within 4Å: Chain B: S.175, F.176, S.249, D.250 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.176 Hydrogen bonds: B:F.176, B:R.188, B:D.250, B:D.250 PGO.5: 3 residues within 4Å: Chain B: Y.5, Y.35 Ligands: IMD.10 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.35 Hydrogen bonds: B:Y.5, B:Y.5 PGO.14: 4 residues within 4Å: Chain D: R.111, R.133, V.194, N.197 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.111, D:R.133, D:V.194 Water bridges: D:R.111 PGO.15: 4 residues within 4Å: Chain D: S.175, F.176, S.249, D.250 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.176 Hydrogen bonds: D:F.176, D:R.188, D:D.250 PGO.16: 3 residues within 4Å: Chain D: Y.5, Y.35 Ligands: IMD.21 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.35 Hydrogen bonds: D:Y.5

2 x ETF: TRIFLUOROETHANOL(Non-covalent)

ETF.6: 3 residues within 4Å: Chain B: H.228, N.232, K.235 1 PLIP interactions: 1 interactions with chain B Halogen bonds: B:N.232 ETF.17: 3 residues within 4Å: Chain D: H.228, N.232, K.235 1 PLIP interactions: 1 interactions with chain D Halogen bonds: D:N.232

10 x IMD: IMIDAZOLE(Non-covalent)

IMD.7: 5 residues within 4Å: Chain B: N.149, Y.170, I.255 Chain D: I.51 Ligands: FLC.2 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.149, B:N.149 pi-Stacking: B:Y.170 IMD.8: 6 residues within 4Å: Chain B: P.144, I.182, F.224, P.226, Y.229 Ligands: FLC.2 No protein-ligand interaction detected (PLIP) IMD.9: 6 residues within 4Å: Chain B: E.129, I.132, I.212, L.254, E.271, K.273 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.273, B:K.273 IMD.10: 3 residues within 4Å: Chain B: Y.35, D.37 Ligands: PGO.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.35 pi-Stacking: B:Y.44 IMD.11: 7 residues within 4Å: Chain B: R.133, V.194, T.196, N.197, K.198, I.200, I.209 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.133, B:T.196 Water bridges: B:I.200 IMD.18: 5 residues within 4Å: Chain B: I.51 Chain D: N.149, Y.170, I.255 Ligands: FLC.13 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.149, D:N.149 Water bridges: D:Y.152 pi-Stacking: D:Y.170 IMD.19: 6 residues within 4Å: Chain D: P.144, I.182, F.224, P.226, Y.229 Ligands: FLC.13 No protein-ligand interaction detected (PLIP) IMD.20: 6 residues within 4Å: Chain D: E.129, I.132, I.212, L.254, E.271, K.273 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.271, D:K.273, D:K.273 IMD.21: 3 residues within 4Å: Chain D: Y.35, D.37 Ligands: PGO.16 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.35, D:Y.35 pi-Stacking: D:Y.44 IMD.22: 7 residues within 4Å: Chain D: R.133, V.194, T.196, N.197, K.198, I.200, I.209 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.133, D:T.196 Water bridges: D:I.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Newberry, K.J. et al., Structures of BmrR-Drug Complexes Reveal a Rigid Multidrug Binding Pocket and Transcription Activation through Tyrosine Expulsion. J.Biol.Chem. (2008)

Release Date

2008-08-26

Peptides

Multidrug-efflux transporter 1 regulator: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

D
A

Multidrug-efflux transporter 1 regulator