SMTL ID : 7f2j.1

Crystal structure of AtFKBP53 FKBD in complex with rapamycin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x RAP: RAPAMYCIN IMMUNOSUPPRESSANT DRUG(Non-covalent)

RAP.1: 16 residues within 4Å: Chain A: Y.35, F.46, D.47, F.55, G.62, S.63, V.64, I.65, W.68, Y.91, I.100, F.108 Chain B: A.96, G.97 Ligands: SO4.5, RAP.6 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.46, A:F.55, A:V.64, A:I.65, A:W.68, A:W.68, A:W.68, A:Y.91, A:I.100, B:A.96 Hydrogen bonds: A:D.47, A:D.47, A:I.65, A:Y.91 RAP.6: 16 residues within 4Å: Chain A: A.96, G.97 Chain B: Y.35, F.46, D.47, F.55, G.62, S.63, V.64, I.65, W.68, Y.91, Q.99, I.100, F.108 Ligands: RAP.1 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.46, B:F.55, B:F.55, B:F.55, B:V.64, B:I.65, B:W.68, B:W.68, B:Y.91, B:Q.99, B:I.100, A:A.96 Hydrogen bonds: B:Y.35, B:D.47, B:I.65, B:Y.91 Water bridges: A:Q.99

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

SO4.2: 2 residues within 4Å: Chain A: K.38, G.43 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.43 Salt bridges: A:K.38 SO4.3: 5 residues within 4Å: Chain A: I.36, K.38, T.107, F.108, D.109 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.109, A:D.109 Salt bridges: A:K.38 SO4.4: 5 residues within 4Å: Chain A: G.51, K.52, S.53 Chain B: P.101, P.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.53, A:S.53 SO4.5: 4 residues within 4Å: Chain A: I.61, G.62, S.63 Ligands: RAP.1 No protein-ligand interaction detected (PLIP) SO4.7: 3 residues within 4Å: Chain B: Q.40, T.84, W.105 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.40

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 5 residues within 4Å: Chain B: S.88, Y.91, G.92, V.93, K.94 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.93, B:K.94 Water bridges: B:S.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, A.K. et al., Crystal packing reveals rapamycin-mediated homodimerization of an FK506-binding domain. Int.J.Biol.Macromol. (2022)

Release Date

2022-03-09

Peptides

Peptidyl-prolyl cis-trans isomerase FKBP53: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Peptidyl-prolyl cis-trans isomerase FKBP53