SMTL ID : 2y31.1

Simocyclinone C4 bound form of TetR-like repressor SimR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x SMQ: SIMOCYCLINONE C4(Non-covalent)

SMQ.1: 19 residues within 4Å: Chain A: M.185, M.189, G.193, Q.197, V.200, L.212, T.215, P.218, H.219 Chain B: K.107, P.126, W.128, Q.135, Q.136, V.139, L.154, I.157, Y.160, N.161 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.128, B:V.139, B:L.154, B:I.157, A:V.200, A:L.212 Hydrogen bonds: B:Q.135, B:N.161, A:H.219 Salt bridges: B:K.107 SMQ.7: 20 residues within 4Å: Chain A: K.107, P.126, W.128, Q.135, Q.136, V.139, L.154, I.157, Y.160, N.161 Chain B: W.174, M.189, G.193, Q.197, V.200, V.211, L.212, T.215, P.218, H.219 13 PLIP interactions: 5 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:W.174, B:M.189, B:V.200, B:L.212, A:W.128, A:V.139, A:L.154 Hydrogen bonds: B:H.219, A:Q.135, A:N.161 Water bridges: A:Q.136, A:Q.136 Salt bridges: A:K.107

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.2: 8 residues within 4Å: Chain A: R.232, D.235, S.236 Chain B: E.152, S.155, S.240, R.243, L.244 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.232 Water bridges: A:R.97, A:A.239

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

PG4.3: 6 residues within 4Å: Chain A: L.88, P.89, D.90, R.134, E.137, F.138 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.88 Water bridges: A:R.91, A:R.134

8 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: W.174, D.184, M.185 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: G.44, V.45, W.116 Chain B: R.122 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: G.221, P.222, D.223, Q.224 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: R.122 Chain B: G.44, V.45, W.116 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: T.70, K.71 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: W.174, D.184, M.185 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: S.49, M.50 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain B: G.221, P.222, D.223, Q.224 Ligand excluded by PLIP

1 x CA: CALCIUM ION(Non-covalent)

CA.8: 1 residues within 4Å: Chain B: D.235 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.235, B:D.235, H2O.9, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Le, T.B.K. et al., Structures of the Tetr-Like Simocyclinone Efflux Pump Repressor, Simr, and the Mechanism of Ligand-Mediated Derepression. J.Mol.Biol. (2011)

Release Date

2011-03-09

Peptides

PUTATIVE REPRESSOR SIMREG2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PUTATIVE REPRESSOR SIMREG2

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