SMTL ID : 3qph.1

The three-dimensional structure of TrmB, a global transcriptional regulator of the hyperthermophilic archaeon Pyrococcus furiosus in complex with sucrose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.99 Å

Oligo State

homo-dimer

Ligands

2 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.1: 14 residues within 4Å: Chain A: F.225, S.229, A.303, V.304, N.305, N.306, G.319, G.320, M.321, F.322, A.323, V.324, I.325, E.326 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.228, A:N.305, A:G.320, A:M.321, A:F.322, A:V.324, A:E.326 Water bridges: A:E.326 GLC-FRU.13: 14 residues within 4Å: Chain B: F.225, S.229, A.303, V.304, N.305, N.306, G.319, G.320, M.321, F.322, A.323, V.324, I.325, E.326 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.305, B:G.320, B:M.321, B:F.322, B:V.324, B:E.326 Water bridges: B:E.326

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 7 residues within 4Å: Chain A: W.112, M.123, E.126, K.217 Chain B: Y.75, S.76 Ligands: GOL.12 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.112 Salt bridges: A:K.217 Hydrogen bonds: B:S.76 ACT.3: 7 residues within 4Å: Chain A: R.125, L.128, Y.129, D.150, K.153, T.154, R.157 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.125, A:Y.129 Salt bridges: A:R.157 ACT.14: 7 residues within 4Å: Chain A: Y.75, S.76 Chain B: W.112, M.123, E.126, K.217 Ligands: GOL.24 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.76 Hydrophobic interactions: B:W.112 Salt bridges: B:K.217 ACT.15: 7 residues within 4Å: Chain B: R.125, L.128, Y.129, D.150, K.153, T.154, R.157 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.125, B:Y.129, B:T.154 Salt bridges: B:R.157

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: N.133, E.275, I.276, T.277, E.332, I.333, K.334 Ligand excluded by PLIP GOL.5: 8 residues within 4Å: Chain A: T.277, G.278, K.279, E.329, S.330, T.331, E.332 Ligands: GOL.8 Ligand excluded by PLIP GOL.6: 4 residues within 4Å: Chain A: L.188, N.189, H.190, L.230 Ligand excluded by PLIP GOL.7: 7 residues within 4Å: Chain A: K.279, L.281, F.322, A.323, V.324, E.329 Ligands: GOL.8 Ligand excluded by PLIP GOL.8: 7 residues within 4Å: Chain A: G.197, M.321, F.322, E.329, T.331 Ligands: GOL.5, GOL.7 Ligand excluded by PLIP GOL.9: 3 residues within 4Å: Chain A: T.290, G.291 Ligands: GOL.10 Ligand excluded by PLIP GOL.10: 6 residues within 4Å: Chain A: A.274, E.275, T.290, K.334, I.336 Ligands: GOL.9 Ligand excluded by PLIP GOL.11: 3 residues within 4Å: Chain A: V.294, G.295, Y.296 Ligand excluded by PLIP GOL.12: 7 residues within 4Å: Chain A: M.123, E.126, S.127, S.130, E.199, K.217 Ligands: ACT.2 Ligand excluded by PLIP GOL.16: 7 residues within 4Å: Chain B: N.133, E.275, I.276, T.277, E.332, I.333, K.334 Ligand excluded by PLIP GOL.17: 8 residues within 4Å: Chain B: T.277, G.278, K.279, E.329, S.330, T.331, E.332 Ligands: GOL.20 Ligand excluded by PLIP GOL.18: 4 residues within 4Å: Chain B: L.188, N.189, H.190, L.230 Ligand excluded by PLIP GOL.19: 7 residues within 4Å: Chain B: K.279, L.281, F.322, A.323, V.324, E.329 Ligands: GOL.20 Ligand excluded by PLIP GOL.20: 7 residues within 4Å: Chain B: G.197, M.321, F.322, E.329, T.331 Ligands: GOL.17, GOL.19 Ligand excluded by PLIP GOL.21: 3 residues within 4Å: Chain B: T.290, G.291 Ligands: GOL.22 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain B: A.274, E.275, T.290, K.334, I.336 Ligands: GOL.21 Ligand excluded by PLIP GOL.23: 3 residues within 4Å: Chain B: V.294, G.295, Y.296 Ligand excluded by PLIP GOL.24: 7 residues within 4Å: Chain B: M.123, E.126, S.127, S.130, E.199, K.217 Ligands: ACT.14 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krug, M. et al., The three-dimensional structure of TrmB, a transcriptional regulator of dual function in the hyperthermophilic archaeon Pyrococcus furiosus in complex with sucrose. Protein Sci. (2013)

Release Date

2012-05-30

Peptides

TrmB, a global transcription regulator: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

TrmB, a global transcription regulator