SMTL ID : 8ckc.1

Vitamin D receptor complex with 25-amine derivative of 1,25D3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-2-mer

Ligands

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 7 residues within 4Å: Chain A: T.23, Y.24, D.25, Y.28, Y.113, K.117, R.151 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.24, A:Y.28 Hydrogen bonds: A:D.25 Salt bridges: A:K.117, A:R.151 ACT.3: 7 residues within 4Å: Chain C: T.23, Y.24, D.25, Y.28, Y.113, K.117, R.151 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:Y.24, C:Y.28 Hydrogen bonds: C:D.25, C:Y.113 Salt bridges: C:K.117, C:R.151

2 x UYU: (1R,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2R)-6-azanyl-6-methyl-heptan-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol(Non-covalent)

UYU.2: 15 residues within 4Å: Chain A: Y.24, L.107, L.110, V.111, S.114, I.148, R.151, S.152, S.155, W.163, C.165, V.177, H.182, L.186, L.289 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.24, A:L.107, A:L.110, A:V.111, A:W.163, A:V.177, A:L.186, A:L.289 Hydrogen bonds: A:S.114, A:R.151, A:S.155 UYU.4: 15 residues within 4Å: Chain C: Y.24, L.107, L.110, V.111, S.114, I.148, R.151, S.152, S.155, W.163, C.165, V.177, H.182, L.186, L.289 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:Y.24, C:L.107, C:L.110, C:V.111, C:W.163, C:V.177, C:L.186, C:L.289 Hydrogen bonds: C:Y.24, C:S.114, C:R.151, C:S.155

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gomez-Bouzo, U. et al., Structural analysis and biological activities of C25-amino and C25-nitro vitamin D analogs. Bioorg.Chem. (2023)

Release Date

2023-04-26

Peptides

Vitamin D3 receptor A: AC
Nuclear receptor coactivator 1: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Vitamin D3 receptor A

Nuclear receptor coactivator 1

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