SMTL ID : 1u8r.1 (1 other biounit)

Crystal Structure of an IdeR-DNA Complex Reveals a Conformational Change in Activated IdeR for Base-specific Interactions

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-tetramer

Ligands

12 x CO: COBALT (II) ION(Non-covalent)

CO.1: 5 residues within 4Å: Chain C: H.79, E.83, H.98, E.172, Q.175 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.79, C:E.83, C:H.98, C:E.172 CO.2: 5 residues within 4Å: Chain C: M.10, R.13, C.102, E.105, H.106 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.102, C:E.105, C:H.106 CO.3: 2 residues within 4Å: Chain C: H.219, H.223 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.219, C:H.223 CO.5: 5 residues within 4Å: Chain D: H.79, E.83, H.98, E.172, Q.175 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:H.79, D:E.83, D:E.83, D:H.98, D:E.172 CO.6: 5 residues within 4Å: Chain D: M.10, R.13, C.102, E.105, H.106 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.102, D:C.102, D:E.105, D:H.106 CO.7: 2 residues within 4Å: Chain D: H.219, H.223 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.219, D:H.223, H2O.1 CO.9: 5 residues within 4Å: Chain E: H.79, E.83, H.98, E.172, Q.175 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.79, E:E.83, E:H.98, E:E.172 CO.10: 5 residues within 4Å: Chain E: M.10, R.13, C.102, E.105, H.106 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.102, E:E.105, E:H.106 CO.11: 2 residues within 4Å: Chain E: H.219, H.223 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.219, E:H.223, H2O.1, H2O.1 CO.13: 5 residues within 4Å: Chain F: H.79, E.83, H.98, E.172, Q.175 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.79, F:E.83, F:H.98, F:E.172 CO.14: 5 residues within 4Å: Chain F: L.4, M.10, C.102, E.105, H.106 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.102, F:E.105, F:H.106 CO.15: 2 residues within 4Å: Chain F: H.219, H.223 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.219, F:H.223, H2O.1

4 x NA: SODIUM ION(Non-functional Binders)

NA.4: 2 residues within 4Å: Chain B: C.19 Chain C: D.35 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.35, C:D.35 NA.8: 2 residues within 4Å: Chain A: C.21 Chain D: D.35 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.35 NA.12: 2 residues within 4Å: Chain A: C.16 Chain E: D.35 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.35, E:D.35 NA.16: 2 residues within 4Å: Chain B: C.24 Chain F: D.35 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:D.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wisedchaisri, G. et al., Crystal Structure of an IdeR-DNA Complex Reveals a Conformational Change in Activated IdeR for Base-specific Interactions. J.Mol.Biol. (2004)

Release Date

2004-10-05

Peptides

Iron-dependent repressor ideR: CDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

D
B

E
C

F
D

Iron-dependent repressor ideR

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