General information
PDB ID 1U8R
Title CRYSTAL STRUCTURE OF AN IDER-DNA COMPLEX REVEALS A CONFORMATIONAL CHANGE IN ACTIVATED IDER FOR BASE-SPECIFIC INTERACTIONS
PDB header METAL-BINDING PROTEIN,TRANSCRIPTION/DNA
Date 2004-08-06
Experimental method X-RAY DIFFRACTION
Resolution (A) 2.75
Kind dna
Organism MYCOBACTERIUM TUBERCULOSIS
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PDB PDBe MMDB Jena OCA
CATH PDBsum HSSP PDBePISA UniProt
ProteopediA BIPA
Composition of PDB entry and biounits
File: Protein chains: DNA chains: RNA chains: No. of models: Action:
PDB entry:
pdb1u8r.pdb ABCDGHIJ EFKL 0
Biounits:
1u8r.pdb1.pdb ABCD EF 1
1u8r.pdb2.pdb GHIJ KL 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Fe_dep_repr_C Domain P9WMH1_65-134 2.4e-29 1 CL0123 A 65 134   
Fe_dep_repress Domain P9WMH1_3-62 3.7e-21 1 CL0123 A 3 62 EF  H-Bb H-Mj L-Bb L-Mj 
DtxR Domain P9WMH1_150-229 5.4e-10 1 CL0206 A 140 229   
Fe_dep_repr_C Domain P9WMH1_65-134 2.4e-29 1 CL0123 B 65 134   
Fe_dep_repress Domain P9WMH1_3-62 3.7e-21 1 CL0123 B 3 62 EF  H-Bb H-Mj L-Bb L-Mj 
DtxR Domain P9WMH1_150-229 5.4e-10 1 CL0206 B 140 229   
Fe_dep_repr_C Domain P9WMH1_65-134 2.4e-29 1 CL0123 C 65 134   
Fe_dep_repress Domain P9WMH1_3-62 3.7e-21 1 CL0123 C 3 62 EF  H-Bb H-Mj L-Bb L-Mj 
DtxR Domain P9WMH1_150-229 5.4e-10 1 CL0206 C 140 229   
Fe_dep_repr_C Domain P9WMH1_65-134 2.4e-29 1 CL0123 D 65 134   
Fe_dep_repress Domain P9WMH1_3-62 3.7e-21 1 CL0123 D 3 62 EF  H-Bb H-Mj L-Bb L-Mj 
DtxR Domain P9WMH1_150-229 5.4e-10 1 CL0206 D 140 229   
Fe_dep_repr_C Domain P9WMH1_65-134 2.4e-29 1 CL0123 G 65 134   
Fe_dep_repress Domain P9WMH1_3-62 3.7e-21 1 CL0123 G 3 62 KL  H-Bb H-Mj L-Bb L-Mj 
DtxR Domain P9WMH1_150-229 5.4e-10 1 CL0206 G 140 229   
Fe_dep_repr_C Domain P9WMH1_65-134 2.4e-29 1 CL0123 H 65 134   
Fe_dep_repress Domain P9WMH1_3-62 3.7e-21 1 CL0123 H 3 62 KL  H-Bb H-Mj L-Bb L-Mj 
DtxR Domain P9WMH1_150-229 5.8e-10 1 CL0206 H 141 229   
Fe_dep_repr_C Domain P9WMH1_65-134 2.4e-29 1 CL0123 I 65 134   
Fe_dep_repress Domain P9WMH1_3-62 3.7e-21 1 CL0123 I 3 62 KL  H-Bb H-Mj L-Bb L-Mj 
DtxR Domain P9WMH1_150-229 5.4e-10 1 CL0206 I 140 229   
Fe_dep_repr_C Domain P9WMH1_65-134 2.4e-29 1 CL0123 J 65 134   
Fe_dep_repress Domain P9WMH1_3-62 3.7e-21 1 CL0123 J 3 62 KL  H-Bb H-Mj L-Bb L-Mj 
DtxR Domain P9WMH1_150-229 5.8e-10 1 CL0206 J 141 229   
SCOP domains
Classification: Protein: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Class: All alpha proteins
  Fold: DNA/RNA-binding 3-helical bundle
    Superfamily: "Winged helix" DNA-binding domain
      Family: Iron-dependent repressor protein
Iron-dependent regulator IdeR A 1 64 EF  H-Bb H-Mj L-Bb L-Mj 
Class: All alpha proteins
  Fold: DNA/RNA-binding 3-helical bundle
    Superfamily: "Winged helix" DNA-binding domain
      Family: Iron-dependent repressor protein
Iron-dependent regulator IdeR B 1 64 EF  H-Bb H-Mj L-Bb L-Mj 
Class: All alpha proteins
  Fold: DNA/RNA-binding 3-helical bundle
    Superfamily: "Winged helix" DNA-binding domain
      Family: Iron-dependent repressor protein
Iron-dependent regulator IdeR C 1 64 EF  H-Bb H-Mj L-Bb L-Mj 
Class: All alpha proteins
  Fold: DNA/RNA-binding 3-helical bundle
    Superfamily: "Winged helix" DNA-binding domain
      Family: Iron-dependent repressor protein
Iron-dependent regulator IdeR D 1 64 EF  H-Bb H-Mj L-Bb L-Mj 
Class: All alpha proteins
  Fold: DNA/RNA-binding 3-helical bundle
    Superfamily: "Winged helix" DNA-binding domain
      Family: Iron-dependent repressor protein
Iron-dependent regulator IdeR G 1 64 KL  H-Bb H-Mj L-Bb L-Mj 
Class: All alpha proteins
  Fold: DNA/RNA-binding 3-helical bundle
    Superfamily: "Winged helix" DNA-binding domain
      Family: Iron-dependent repressor protein
Iron-dependent regulator IdeR H 1 64 KL  H-Bb H-Mj L-Bb L-Mj 
Class: All alpha proteins
  Fold: DNA/RNA-binding 3-helical bundle
    Superfamily: "Winged helix" DNA-binding domain
      Family: Iron-dependent repressor protein
Iron-dependent regulator IdeR I 1 64 KL  H-Bb H-Mj L-Bb L-Mj 
Class: All alpha proteins
  Fold: DNA/RNA-binding 3-helical bundle
    Superfamily: "Winged helix" DNA-binding domain
      Family: Iron-dependent repressor protein
Iron-dependent regulator IdeR J 1 64 KL  H-Bb H-Mj L-Bb L-Mj 
Class: All alpha proteins
  Fold: Iron-dependent repressor protein, dimerization domain
    Superfamily: Iron-dependent repressor protein, dimerization domain
      Family: Iron-dependent repressor protein, dimerization domain
Iron-dependent regulator A 65 141 -
Class: All beta proteins
  Fold: SH3-like barrel
    Superfamily: C-terminal domain of transcriptional repressors
      Family: FeoA-like
Iron-dependent regulator IdeR A 151 230 -
Class: All alpha proteins
  Fold: Iron-dependent repressor protein, dimerization domain
    Superfamily: Iron-dependent repressor protein, dimerization domain
      Family: Iron-dependent repressor protein, dimerization domain
Iron-dependent regulator B 65 141 -
Class: All beta proteins
  Fold: SH3-like barrel
    Superfamily: C-terminal domain of transcriptional repressors
      Family: FeoA-like
Iron-dependent regulator IdeR B 151 230 -
Class: All alpha proteins
  Fold: Iron-dependent repressor protein, dimerization domain
    Superfamily: Iron-dependent repressor protein, dimerization domain
      Family: Iron-dependent repressor protein, dimerization domain
Iron-dependent regulator C 65 141 -
Class: All beta proteins
  Fold: SH3-like barrel
    Superfamily: C-terminal domain of transcriptional repressors
      Family: FeoA-like
Iron-dependent regulator IdeR C 151 230 -
Class: All alpha proteins
  Fold: Iron-dependent repressor protein, dimerization domain
    Superfamily: Iron-dependent repressor protein, dimerization domain
      Family: Iron-dependent repressor protein, dimerization domain
Iron-dependent regulator D 65 141 -
Class: All beta proteins
  Fold: SH3-like barrel
    Superfamily: C-terminal domain of transcriptional repressors
      Family: FeoA-like
Iron-dependent regulator IdeR D 151 230 -
Class: All alpha proteins
  Fold: Iron-dependent repressor protein, dimerization domain
    Superfamily: Iron-dependent repressor protein, dimerization domain
      Family: Iron-dependent repressor protein, dimerization domain
Iron-dependent regulator G 65 141 -
Class: All beta proteins
  Fold: SH3-like barrel
    Superfamily: C-terminal domain of transcriptional repressors
      Family: FeoA-like
Iron-dependent regulator IdeR G 151 230 -
Class: All alpha proteins
  Fold: Iron-dependent repressor protein, dimerization domain
    Superfamily: Iron-dependent repressor protein, dimerization domain
      Family: Iron-dependent repressor protein, dimerization domain
Iron-dependent regulator H 65 141 -
Class: All beta proteins
  Fold: SH3-like barrel
    Superfamily: C-terminal domain of transcriptional repressors
      Family: FeoA-like
Iron-dependent regulator IdeR H 150 230 -
Class: All alpha proteins
  Fold: Iron-dependent repressor protein, dimerization domain
    Superfamily: Iron-dependent repressor protein, dimerization domain
      Family: Iron-dependent repressor protein, dimerization domain
Iron-dependent regulator I 65 141 -
Class: All beta proteins
  Fold: SH3-like barrel
    Superfamily: C-terminal domain of transcriptional repressors
      Family: FeoA-like
Iron-dependent regulator IdeR I 151 230 -
Class: All alpha proteins
  Fold: Iron-dependent repressor protein, dimerization domain
    Superfamily: Iron-dependent repressor protein, dimerization domain
      Family: Iron-dependent repressor protein, dimerization domain
Iron-dependent regulator J 65 141 -
Class: All beta proteins
  Fold: SH3-like barrel
    Superfamily: C-terminal domain of transcriptional repressors
      Family: FeoA-like
Iron-dependent regulator IdeR J 150 230 -
GO terms
Protein chains: GO type: GO description:
A/B/C/D/G/H/I/J=1-230 C extracellular region
A/B/C/D/G/H/I/J=1-230 C cell wall
A/B/C/D/G/H/I/J=1-230 C cytoplasm
A/B/C/D/G/H/I/J=1-230 C plasma membrane
A/B/C/D/G/H/I/J=1-230 F peptidoglycan L,D-transpeptidase activity
A/B/C/D/G/H/I/J=1-230 F transferase activity, transferring acyl groups
A/B/C/D/G/H/I/J=1-230 F cadmium ion binding
A/B/C/D/G/H/I/J=1-230 F cobalt ion binding
A/B/C/D/G/H/I/J=1-230 F DNA binding
A/B/C/D/G/H/I/J=1-230 F DNA-binding transcription factor activity
A/B/C/D/G/H/I/J=1-230 F ferrous iron binding
A/B/C/D/G/H/I/J=1-230 F iron ion binding
A/B/C/D/G/H/I/J=1-230 F manganese ion binding
A/B/C/D/G/H/I/J=1-230 F nickel cation binding
A/B/C/D/G/H/I/J=1-230 F protein dimerization activity
A/B/C/D/G/H/I/J=1-230 F zinc ion binding
A/B/C/D/G/H/I/J=1-230 P cell wall organization
A/B/C/D/G/H/I/J=1-230 P peptidoglycan-protein cross-linking
A/B/C/D/G/H/I/J=1-230 P regulation of cell shape
A/B/C/D/G/H/I/J=1-230 P negative regulation of transcription, DNA-templated
A/B/C/D/G/H/I/J=1-230 P regulation of transcription, DNA-templated
A/B/C/D/G/H/I/J=1-230 P response to oxidative stress
A/B/C/D/G/H/I/J=1-230 P siderophore biosynthetic process from catechol
Sequences
Download file with secondary structure created by Stride  
1u8r.pdb1.pdb:   [ download sequences in FASTA format ]
E (dna): 
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F (dna): 
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A (protein): 
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B (protein): 
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C (protein): 
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D (protein): 
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1u8r.pdb2.pdb:   [ download sequences in FASTA format ]
K (dna): 
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L (dna): 
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G (protein): 
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H (protein): 
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I (protein): 
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J (protein): 
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