SMTL ID : 2rha.1

Crystal structure of a predicted dna-binding transcriptional regulator (saro_1072) from novosphingobium aromaticivorans dsm at 2.10 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 1 residues within 4Å: Chain A: R.95 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: H.201 Chain B: I.158, N.159 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain B: R.95 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain A: I.158, N.159 Chain B: H.201 Ligand excluded by PLIP

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 7 residues within 4Å: Chain A: R.30, E.31, L.179, K.182, H.183 Ligands: SO4.6, GOL.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.30 Water bridges: A:K.182 Salt bridges: A:K.182, A:H.183 SO4.4: 5 residues within 4Å: Chain A: P.15, G.16, A.17, R.18, D.19 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.16, A:R.18, A:D.19 Water bridges: A:A.17, A:A.17 SO4.5: 1 residues within 4Å: Chain B: H.201 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.201 SO4.6: 8 residues within 4Å: Chain A: R.30, Y.106, L.179, K.182, D.188, L.190 Ligands: SO4.3, GOL.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.106 Water bridges: A:R.30 Salt bridges: A:R.30, A:K.182 SO4.20: 7 residues within 4Å: Chain B: R.30, E.31, L.179, K.182, H.183 Ligands: SO4.23, GOL.31 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.30 Water bridges: B:K.182 Salt bridges: B:K.182, B:H.183 SO4.21: 5 residues within 4Å: Chain B: P.15, G.16, A.17, R.18, D.19 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.16, B:R.18, B:D.19 Water bridges: B:A.17, B:A.17 SO4.22: 1 residues within 4Å: Chain A: H.201 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.201 SO4.23: 8 residues within 4Å: Chain B: R.30, Y.106, L.179, K.182, D.188, L.190 Ligands: SO4.20, GOL.27 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.106, B:Y.106 Water bridges: B:R.30 Salt bridges: B:R.30, B:K.182

22 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: V.35, R.117, R.120 Chain B: V.34, V.35 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: S.38, L.39, S.40, K.60 Ligand excluded by PLIP GOL.9: 7 residues within 4Å: Chain A: A.131, D.132, Y.134, L.135, L.136, H.139 Ligands: GOL.17 Ligand excluded by PLIP GOL.10: 5 residues within 4Å: Chain A: R.30, Y.106, D.107 Ligands: SO4.6, GOL.14 Ligand excluded by PLIP GOL.11: 3 residues within 4Å: Chain A: T.191, E.192, Q.193 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain A: T.24, N.27, E.31, R.45 Ligand excluded by PLIP GOL.13: 7 residues within 4Å: Chain A: R.113, D.172, R.173, S.176 Chain B: N.112, R.113, M.116 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain A: N.27, R.30, E.31 Ligands: SO4.3, GOL.10 Ligand excluded by PLIP GOL.15: 3 residues within 4Å: Chain A: S.89, E.91, A.92 Ligand excluded by PLIP GOL.16: 3 residues within 4Å: Chain A: R.178 Chain B: N.159, Q.161 Ligand excluded by PLIP GOL.17: 7 residues within 4Å: Chain A: K.128, A.131, D.132, L.135 Chain B: F.185, Q.187 Ligands: GOL.9 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain A: V.34, V.35 Chain B: V.35, R.117, R.120 Ligand excluded by PLIP GOL.25: 4 residues within 4Å: Chain B: S.38, L.39, S.40, K.60 Ligand excluded by PLIP GOL.26: 7 residues within 4Å: Chain B: A.131, D.132, Y.134, L.135, L.136, H.139 Ligands: GOL.34 Ligand excluded by PLIP GOL.27: 5 residues within 4Å: Chain B: R.30, Y.106, D.107 Ligands: SO4.23, GOL.31 Ligand excluded by PLIP GOL.28: 3 residues within 4Å: Chain B: T.191, E.192, Q.193 Ligand excluded by PLIP GOL.29: 4 residues within 4Å: Chain B: T.24, N.27, E.31, R.45 Ligand excluded by PLIP GOL.30: 7 residues within 4Å: Chain A: N.112, R.113, M.116 Chain B: R.113, D.172, R.173, S.176 Ligand excluded by PLIP GOL.31: 5 residues within 4Å: Chain B: N.27, R.30, E.31 Ligands: SO4.20, GOL.27 Ligand excluded by PLIP GOL.32: 3 residues within 4Å: Chain B: S.89, E.91, A.92 Ligand excluded by PLIP GOL.33: 3 residues within 4Å: Chain A: N.159, Q.161 Chain B: R.178 Ligand excluded by PLIP GOL.34: 7 residues within 4Å: Chain A: F.185, Q.187 Chain B: K.128, A.131, D.132, L.135 Ligands: GOL.26 Ligand excluded by PLIP

Links

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Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of predicted DNA-binding transcriptional regulator (YP_496351.1) from Novosphingobium aromaticivorans DSM 12444 at 2.10 A resolution. To be published

Release Date

2007-10-30

Peptides

Transcriptional regulator, TetR family: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Transcriptional regulator, TetR family

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