SMTL ID : 5uc1.1

Structural Analysis of Glucocorticoid Receptor beta Ligand Binding Domain Complexed with Glucocorticoid Antagonist RU-486: Implication of Helix 12 in Antagonism

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

2 x 486: 11-(4-DIMETHYLAMINO-PHENYL)-17-HYDROXY-13-METHYL-17-PROP-1-YNYL-1,2,6,7,8,11,12,13,14,15,16,17-DODEC AHYDRO-CYCLOPENTA[A]PHENANTHREN-3-ONE(Non-covalent)

486.1: 20 residues within 4Å: Chain A: L.43, N.44, L.46, G.47, G.48, Q.50, V.51, W.80, M.84, A.85, L.88, R.91, F.103, Q.122, C.123, M.126 Chain B: W.37, M.40, N.44 Ligands: 486.9 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.43, A:L.43, A:L.46, A:M.84, A:F.103, A:Q.122 Hydrogen bonds: A:Q.50, A:R.91 Water bridges: A:R.91 486.9: 19 residues within 4Å: Chain A: W.37, M.40, N.44 Chain B: L.43, N.44, L.46, G.47, G.48, Q.50, V.51, M.84, A.85, L.88, R.91, F.103, Q.122, C.123, M.126 Ligands: 486.1 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.43, B:L.43, B:L.46, B:M.84, B:F.103 Hydrogen bonds: B:Q.50, B:R.91

4 x CPS: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE(Non-covalent)

CPS.2: 8 residues within 4Å: Chain A: T.35, W.37 Chain B: V.51, I.52, L.76, Q.77, W.80 Ligands: CL.12 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:V.51, B:L.76, A:W.37, A:W.37, A:W.37 Hydrogen bonds: B:Q.77 CPS.3: 13 residues within 4Å: Chain A: M.81, S.82, A.85, Q.125, M.126, F.128, S.204, M.205, E.207, N.208 Chain B: Y.118, D.121, Q.122 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:A.85, A:F.128, B:Y.118, B:D.121 Hydrogen bonds: A:Q.125, A:N.208 CPS.10: 8 residues within 4Å: Chain A: V.51, M.73, L.76, Q.77, W.80 Chain B: T.35, W.37 Ligands: CL.4 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.37, B:W.37, B:W.37, A:V.51, A:L.76 CPS.11: 12 residues within 4Å: Chain A: Y.118, D.121, Q.122 Chain B: S.82, A.85, Q.125, M.126, F.128, S.204, M.205, E.207, N.208 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:A.85, B:Q.125, B:F.128, B:F.128, B:E.207, A:Y.118, A:D.121 Hydrogen bonds: B:Q.125, B:E.207, A:D.121

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

CL.4: 6 residues within 4Å: Chain A: Q.77 Chain B: T.35, T.36, L.116, P.117 Ligands: CPS.10 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: S.162, Q.163, E.164, L.165 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain A: T.35, T.36, P.117 Chain B: Q.77 Ligands: CPS.2 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain B: S.162, Q.163, E.164, L.165 Ligand excluded by PLIP

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6: 2 residues within 4Å: Chain A: P.62, G.63 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.62 MPD.14: 1 residues within 4Å: Chain B: G.63 No protein-ligand interaction detected (PLIP)

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 1 residues within 4Å: Chain A: K.147 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.147, A:K.147 EDO.8: 3 residues within 4Å: Chain A: G.178, N.191, W.192 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.191 EDO.15: 1 residues within 4Å: Chain B: K.147 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.147, B:K.147 EDO.16: 3 residues within 4Å: Chain B: G.178, N.191, W.192 No protein-ligand interaction detected (PLIP) EDO.17: 6 residues within 4Å: Chain B: E.132, R.135, Q.197, K.200, L.201, S.204 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.135, B:Q.197, B:L.201, B:S.204

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Min, J. et al., Probing Dominant Negative Behavior of Glucocorticoid Receptor beta through a Hybrid Structural and Biochemical Approach. Mol. Cell. Biol. (2018)

Release Date

2017-12-27

Peptides

Glucocorticoid receptor: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glucocorticoid receptor