SMTL ID : 4cn2.1

Crystal Structure of the Human Retinoid X Receptor DNA-Binding Domain Bound to the Human Ramp2 Response Element

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-dimer

Ligands

7 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: T.1, G.2 Chain C: G.19, K.20, H.21 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:K.20, H2O.2 MG.2: 3 residues within 4Å: Chain A: A.9, G.10 Chain D: H.21 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.21, H2O.2 MG.3: 3 residues within 4Å: Chain B: T.9, T.10 Chain C: K.40 No protein-ligand interaction detected (PLIP) MG.8: 8 residues within 4Å: Chain B: G.11, A.12 Chain C: D.15, C.27, E.28, G.29, R.59 Ligands: MG.10 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain C: L.71, G.74, M.75, K.76 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:L.71, C:M.75 MG.10: 5 residues within 4Å: Chain B: A.12 Chain C: D.15, K.56, R.59 Ligands: MG.8 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.15, H2O.5 MG.16: 5 residues within 4Å: Chain B: T.3, G.4 Chain D: G.29, F.33, R.36 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:G.29

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain C: C.10, C.13, C.27, C.30 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.10, C:C.13, C:C.27, C:C.30 ZN.5: 4 residues within 4Å: Chain C: C.46, C.52, C.62, C.65 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.46, C:C.52, C:C.62, C:C.65 ZN.11: 4 residues within 4Å: Chain D: C.10, C.13, C.27, C.30 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.10, D:C.13, D:C.27, D:C.30 ZN.12: 4 residues within 4Å: Chain D: C.46, C.52, C.62, C.65 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.46, D:C.52, D:C.62, D:C.65

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.6: 9 residues within 4Å: Chain C: T.37, D.41, L.42, T.43, Y.44, Y.64, Y.67, Q.68, R.77 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.44, C:Y.64, C:Q.68, C:R.77

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

CL.7: 2 residues within 4Å: Chain C: V.24, Y.25 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain D: R.47, R.61, C.62, Q.63 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain A: G.10 Chain B: T.10 Chain D: Q.81, R.84 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain D: Y.44, T.45 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osz, J. et al., Structural Basis of Natural Promoter Recognition by the Retinoid X Nuclear Receptor. Sci.Rep. (2015)

Release Date

2015-02-18

Peptides

RETINOIC ACID RECEPTOR RXR-ALPHA: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
C

D
D

RETINOIC ACID RECEPTOR RXR-ALPHA

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