SMTL ID : 5uc3.1

Structure of the dominant negative mutant Glucocorticoid Receptor alpha (L733K/N734P) complexed with RU-486

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-tetramer

Ligands

4 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: 18 residues within 4Å: Chain A: M.40, L.43, N.44, L.46, G.47, Q.50, W.80, M.81, M.84, R.91, F.103, M.119, Q.122, M.126, L.212, Y.215, C.216 Chain C: F.220 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.43, A:L.46, A:W.80, A:F.103, A:F.103, A:L.212 Hydrogen bonds: A:Q.50, A:R.91 Water bridges: A:R.91 486.11: 17 residues within 4Å: Chain B: M.40, L.43, N.44, G.47, Q.50, V.51, W.80, M.81, M.84, R.91, F.103, Q.122, M.126, L.212, Y.215, C.216 Chain D: F.220 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.43, B:W.80, B:F.103, B:F.103, B:L.212 Hydrogen bonds: B:Q.50, B:R.91 Water bridges: B:R.91 486.16: 18 residues within 4Å: Chain A: F.220 Chain C: M.40, L.43, N.44, L.46, G.47, Q.50, W.80, M.81, M.84, R.91, F.103, M.119, Q.122, M.126, L.212, Y.215, C.216 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:L.43, C:L.46, C:W.80, C:F.103, C:F.103, C:L.212 Hydrogen bonds: C:Q.50, C:R.91 Water bridges: C:R.91 486.26: 17 residues within 4Å: Chain B: F.220 Chain D: M.40, L.43, N.44, G.47, Q.50, V.51, W.80, M.81, M.84, R.91, F.103, Q.122, M.126, L.212, Y.215, C.216 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:L.43, D:W.80, D:F.103, D:F.103, D:L.212 Hydrogen bonds: D:Q.50, D:R.91 Water bridges: D:R.91

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

MPD.2: 9 residues within 4Å: Chain A: E.20, P.21, Q.50, A.53, W.57, M.84, A.87, R.91, K.147 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.57, A:A.87, A:K.147 Hydrogen bonds: A:Q.50, A:K.147 MPD.3: 5 residues within 4Å: Chain A: H.125, Y.128, E.207, V.208, N.211 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.128, A:E.207, A:V.208 Hydrogen bonds: A:H.125, A:N.211 MPD.12: 8 residues within 4Å: Chain B: E.20, P.21, Q.50, W.57, L.83, A.87, R.91, K.147 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Q.50, B:W.57, B:L.83, B:K.147 Hydrogen bonds: B:K.147 Water bridges: B:E.20 MPD.17: 9 residues within 4Å: Chain C: E.20, P.21, Q.50, A.53, W.57, M.84, A.87, R.91, K.147 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.57, C:A.87, C:K.147 Hydrogen bonds: C:Q.50, C:K.147 MPD.18: 5 residues within 4Å: Chain C: H.125, Y.128, E.207, V.208, N.211 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.128, C:E.207, C:V.208 Hydrogen bonds: C:H.125, C:N.211 MPD.27: 8 residues within 4Å: Chain D: E.20, P.21, Q.50, W.57, L.83, A.87, R.91, K.147 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:Q.50, D:W.57, D:L.83, D:K.147 Hydrogen bonds: D:K.147 Water bridges: D:E.20, D:E.20

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

EDO.4: 2 residues within 4Å: Chain A: S.97, H.134 Ligand excluded by PLIP EDO.5: 2 residues within 4Å: Chain C: K.223, T.224 Ligand excluded by PLIP EDO.6: 2 residues within 4Å: Chain A: Y.93, V.138 Ligand excluded by PLIP EDO.7: 1 residues within 4Å: Chain A: M.73 Ligand excluded by PLIP EDO.8: 1 residues within 4Å: Chain A: F.254 Ligand excluded by PLIP EDO.9: 2 residues within 4Å: Chain A: W.90, R.94 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain B: H.125, Y.128, N.211 Ligand excluded by PLIP EDO.14: 1 residues within 4Å: Chain D: M.45 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain D: K.223, T.224 Ligand excluded by PLIP EDO.19: 2 residues within 4Å: Chain C: S.97, H.134 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain A: K.223, T.224 Ligand excluded by PLIP EDO.21: 2 residues within 4Å: Chain C: Y.93, V.138 Ligand excluded by PLIP EDO.22: 1 residues within 4Å: Chain C: M.73 Ligand excluded by PLIP EDO.23: 1 residues within 4Å: Chain C: F.254 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain C: W.90, R.94 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain D: H.125, Y.128, N.211 Ligand excluded by PLIP EDO.29: 1 residues within 4Å: Chain B: M.45 Ligand excluded by PLIP EDO.30: 2 residues within 4Å: Chain B: K.223, T.224 Ligand excluded by PLIP

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.10: 4 residues within 4Å: Chain A: G.178, V.182, N.191, F.195 2 PLIP interactions: 2 interactions with chain A Water bridges: A:W.192 pi-Cation interactions: A:F.195 EPE.25: 4 residues within 4Å: Chain C: G.178, V.182, N.191, F.195 2 PLIP interactions: 2 interactions with chain C Water bridges: C:W.192 pi-Cation interactions: C:F.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Min, J. et al., Nuclear receptor. To Be Published

Release Date

2017-12-27

Peptides

Glucocorticoid receptor: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Glucocorticoid receptor