SMTL ID : 5jjm.2 (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: 9 residues within 4Å: Chain A: C.2, D.172, A.176, R.179, K.180, N.181, P.182, C.185 Ligands: ZN.6 No protein-ligand interaction detected (PLIP) FME-SER-ASP.2: 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.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.1, B:C.2

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

SER-LEU-GLN-PHE-LEU-LEU-ASP-THR.3: 7 residues within 4Å: Chain A: V.46, V.49, K.53, Q.66, M.67, Q.71, M.227 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.46, A:V.49, A:V.49, A:K.53, A:Q.71 Hydrogen bonds: A:K.53, A:E.230 SER-LEU-GLN-PHE-LEU-LEU-ASP-THR.4: 6 residues within 4Å: Chain B: V.46, V.49, K.53, Q.66, M.67, M.227 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.46, B:V.49, B:V.49, B:K.53, B:Q.66

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

DHT.5: 15 residues within 4Å: Chain A: L.34, L.37, N.38, L.40, G.41, Q.44, M.75, M.78, V.79, M.82, R.85, F.97, M.113, T.210, F.224 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.34, A:M.78, A:V.79, A:F.97, A:F.97 Hydrogen bonds: A:N.38, A:Q.44, A:R.85, A:T.210 DHT.12: 12 residues within 4Å: Chain B: L.34, L.37, N.38, L.40, Q.44, M.75, M.78, M.82, R.85, F.97, T.210, F.224 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.34, B:L.40, B:M.78, B:F.97, B:F.97 Hydrogen bonds: B:N.38, B:Q.44, B:R.85 Water bridges: B:M.82

2 x ZN: ZINC ION(Non-covalent)

ZN.6: 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.13: 3 residues within 4Å: Chain B: C.185 Ligands: FME-SER-ASP.2, FME-SER-ASP.2 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.185

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

CL.7: 3 residues within 4Å: Chain A: K.180, N.181, S.184 Ligand excluded by PLIP

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

EDO.8: 5 residues within 4Å: Chain A: F.87, T.88, N.91 Chain B: W.84, L.138 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:W.84, A:N.91 EDO.9: 2 residues within 4Å: Chain A: G.21, R.43 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.43, A:R.43 EDO.10: 2 residues within 4Å: Chain A: R.179, S.184 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.179, A:S.184 EDO.14: 2 residues within 4Å: Chain B: G.21, R.43 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.43, B:R.43

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

SO4.11: 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:K.110, A:R.112 Salt bridges: A:K.110, A:R.112 SO4.17: 4 residues within 4Å: Chain B: S.29, F.30, K.110, R.112 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:F.30 Water bridges: B:R.112, B:R.112 Salt bridges: B:K.110, B:R.112 SO4.18: 2 residues within 4Å: Chain B: R.112, V.220 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.112

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 8 residues within 4Å: Chain A: E.14, W.84, P.134, F.137, 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:E.14, B:T.88, B:N.91

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.16: 2 residues within 4Å: Chain B: H.109, K.110 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.110

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
B

B
C

Androgen receptor

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