SMTL ID : 6oqa.2 (1 other biounit)

Crystal structure of CEP250 bound to FKBP12 in the presence of FK506-like novel natural product

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-2-2-mer

Ligands

2 x 60Z: (3R,4E,7E,10R,11S,12R,13S,16R,17R,24aS)-11,17-dihydroxy-10,12,16-trimethyl-3-[(2R)-1-phenylbutan-2-yl]-6,9,10,11,12,13,14,15,16,17,22,23,24,24a-tetradecahydro-3H-13,17-epoxypyrido[2,1-c][1,4]oxazacyclohenicosine-1,18,19(21H)-trione(Non-covalent)

60Z.1: 21 residues within 4Å: Chain A: Y.27, F.37, D.38, F.47, Q.54, E.55, V.56, I.57, W.60, Y.83, H.88, I.92, F.100 Chain C: L.57, V.60, F.63 Chain D: Q.58, A.61, M.62, Q.65 Ligands: PGE.9 20 PLIP interactions: 15 interactions with chain A, 3 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: A:Y.27, A:F.37, A:F.47, A:F.47, A:I.57, A:W.60, A:W.60, A:Y.83, A:I.92, C:L.57, C:V.60, C:F.63, D:Q.65, D:Q.65 Hydrogen bonds: A:Y.27, A:D.38, A:D.38, A:D.38, A:I.57, A:Y.83 60Z.4: 21 residues within 4Å: Chain B: Y.27, F.37, D.38, F.47, Q.54, E.55, V.56, I.57, W.60, Y.83, H.88, I.92, F.100 Chain C: Q.58, A.61, M.62, Q.65 Chain D: L.57, V.60, F.63, L.64 20 PLIP interactions: 13 interactions with chain B, 3 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: B:F.37, B:F.47, B:I.57, B:W.60, B:W.60, B:Y.83, B:I.92, C:Q.58, C:Q.65, C:Q.65, D:V.60, D:V.60, D:F.63, D:L.64 Hydrogen bonds: B:Y.27, B:D.38, B:D.38, B:D.38, B:I.57, B:Y.83

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

EDO.2: 3 residues within 4Å: Chain A: K.53, Q.54 Chain C: R.71 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.54 EDO.3: 4 residues within 4Å: Chain A: D.80, A.82, Y.83, G.84 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.80, A:D.80 EDO.6: 2 residues within 4Å: Chain C: E.18 Chain D: Q.23 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.18, C:E.18

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

PEG.5: 4 residues within 4Å: Chain B: K.45 Chain C: E.59, M.62, F.63 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.45 PEG.7: 3 residues within 4Å: Chain C: Q.23, A.24, R.27 No protein-ligand interaction detected (PLIP) PEG.11: 2 residues within 4Å: Chain D: E.35, W.36 No protein-ligand interaction detected (PLIP)

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.8: 3 residues within 4Å: Chain C: E.30, E.33 Chain D: R.32 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.30, D:R.32

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

PGE.9: 5 residues within 4Å: Chain A: T.86, H.88 Chain C: E.59, F.63 Ligands: 60Z.1 No protein-ligand interaction detected (PLIP)

1 x MLA: MALONIC ACID(Non-covalent)

MLA.10: 4 residues within 4Å: Chain C: R.21, L.22 Chain D: Q.23, R.27 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Q.23 Hydrogen bonds: D:Q.23 Water bridges: D:R.27 Salt bridges: D:R.27, C:R.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shigdel, U.K. et al., Genomic discovery of an evolutionarily programmed modality for small-molecule targeting of an intractable protein surface. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-04-29

Peptides

Peptidyl-prolyl cis-trans isomerase FKBP1A: AB
Centrosome-associated protein CEP250: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

Peptidyl-prolyl cis-trans isomerase FKBP1A

Centrosome-associated protein CEP250

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