SMTL ID : 5jjm.1 (2 other biounits)

Crystal Structure of Homodimeric Androgen Receptor Ligand-Binding Domain bound to DHT and LxxLL peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

2 x FME- SER- ASP: Unknown peptide(Non-covalent)

FME-SER-ASP.1: 10 residues within 4Å: Chain A: E.1, C.2, D.172, A.176, R.179, K.180, N.181, P.182, C.185 Ligands: ZN.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.1, A:C.2 FME-SER-ASP.9: 10 residues within 4Å: Chain B: E.1, C.2, D.172, A.176, R.179, K.180, N.181, P.182, C.185 Ligands: ZN.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:C.2

2 x SER- LEU- GLN- PHE- LEU- LEU- ASP: uba3-derived peptide(Non-covalent)

SER-LEU-GLN-PHE-LEU-LEU-ASP.2: 9 residues within 4Å: Chain A: V.46, V.49, K.53, V.63, Q.66, M.67, Q.71, M.227, I.231 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.46, A:V.49, A:K.53, A:Q.66, A:Q.71, A:I.231 SER-LEU-GLN-PHE-LEU-LEU-ASP.10: 9 residues within 4Å: Chain B: V.46, V.49, K.53, V.63, Q.66, M.67, Q.71, M.227, I.231 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.46, B:V.49, B:K.53, B:Q.66, B:Q.71, B:I.231

2 x DHT: 5-ALPHA-DIHYDROTESTOSTERONE(Non-covalent)

DHT.3: 15 residues within 4Å: Chain A: L.34, L.37, N.38, L.40, Q.44, M.75, M.78, V.79, M.82, R.85, F.97, M.113, T.210, F.224, M.228 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.34, A:L.40, A:M.78, A:V.79, A:F.97 Hydrogen bonds: A:N.38, A:Q.44, A:R.85 Water bridges: A:M.82 DHT.11: 15 residues within 4Å: Chain B: L.34, L.37, N.38, L.40, Q.44, M.75, M.78, V.79, M.82, R.85, F.97, M.113, T.210, F.224, M.228 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.34, B:L.40, B:M.78, B:V.79, B:F.97 Hydrogen bonds: B:N.38, B:Q.44, B:R.85, B:T.210 Water bridges: B:M.82

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: P.182, C.185 Ligands: FME-SER-ASP.1, FME-SER-ASP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.185 ZN.12: 4 residues within 4Å: Chain B: P.182, C.185 Ligands: FME-SER-ASP.9, FME-SER-ASP.9 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.185

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

CL.5: 3 residues within 4Å: Chain A: K.180, N.181, S.184 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: K.180, N.181, S.184 Ligand excluded by PLIP

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

EDO.6: 3 residues within 4Å: Chain A: C.19, G.21, R.43 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.43, A:R.43 EDO.14: 3 residues within 4Å: Chain B: C.19, G.21, R.43 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.43, B:R.43

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: F.87, T.88, N.91 Chain B: E.14, W.84, L.138 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:W.84, A:N.91, A:N.91 GOL.15: 6 residues within 4Å: Chain A: E.14, W.84, L.138 Chain B: F.87, T.88, N.91 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:W.84, B:N.91, B:N.91

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 4 residues within 4Å: Chain A: S.29, F.30, K.110, R.112 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.30 Water bridges: A:A.31, A:R.112, A:R.112 Salt bridges: A:K.110, A:R.112 SO4.16: 4 residues within 4Å: Chain B: S.29, F.30, K.110, R.112 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:F.30 Water bridges: B:A.31, B:R.112, B:R.112 Salt bridges: B:K.110, B:R.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nadal, M. et al., Structure of the homodimeric androgen receptor ligand-binding domain. Nat Commun (2017)

Release Date

2017-03-15

Peptides

Androgen receptor: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Androgen receptor

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