SMTL ID : 6oqa.1 (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: 23 residues within 4Å: Chain A: Y.27, F.37, D.38, R.43, 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, L.64 Chain D: Q.58, A.61, M.62, Q.65 Ligands: PG4.22 23 PLIP interactions: 15 interactions with chain A, 4 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: A:Y.27, A:F.37, A:F.47, A:I.57, A:W.60, A:Y.83, A:Y.83, A:I.92, C:L.57, C:V.60, C:F.63, C:L.64, D:A.61, D:Q.65, D:Q.65 Hydrogen bonds: A:Y.27, A:D.38, A:D.38, A:D.38, A:R.43, A:I.57, A:Y.83, D:Q.58 60Z.7: 22 residues within 4Å: Chain B: Y.27, F.37, D.38, R.43, 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 Ligands: PE8.18 23 PLIP interactions: 17 interactions with chain B, 4 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: B:Y.27, B:F.37, B:F.47, B:F.47, B:F.47, B:I.57, B:W.60, B:W.60, B:Y.83, B:Y.83, B:I.92, C:A.61, C:Q.65, C:Q.65, D:V.60, D:F.63 Hydrogen bonds: B:Y.27, B:D.38, B:D.38, B:D.38, B:I.57, B:Y.83, C:Q.58

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

EDO.2: 5 residues within 4Å: Chain A: D.80, A.82, Y.83, G.84 Ligands: PG4.22 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.86 EDO.3: 3 residues within 4Å: Chain A: Q.21, L.107, E.108 No protein-ligand interaction detected (PLIP) EDO.4: 3 residues within 4Å: Chain A: M.1, G.2, T.76 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.76 EDO.8: 3 residues within 4Å: Chain B: H.26, R.41, N.44 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.41, B:N.44, B:N.44 EDO.9: 1 residues within 4Å: Chain B: K.106 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.106 EDO.10: 2 residues within 4Å: Chain B: L.105, K.106 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.106 EDO.11: 2 residues within 4Å: Chain B: K.53 Chain D: R.71 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.53 EDO.12: 3 residues within 4Å: Chain B: S.78, P.79, D.80 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.80, B:D.80 EDO.13: 2 residues within 4Å: Chain B: T.7, I.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.7 EDO.14: 3 residues within 4Å: Chain B: E.6, I.8, K.74 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.6 Water bridges: B:K.74 EDO.20: 4 residues within 4Å: Chain C: D.42, L.45, S.46, Q.49 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.42, C:S.46, C:Q.49 EDO.27: 5 residues within 4Å: Chain B: K.35, G.90, I.91, P.93 Chain D: Q.49 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:Q.49, B:K.35, B:K.35, B:G.90 EDO.28: 1 residues within 4Å: Chain D: Q.79 1 PLIP interactions: 1 interactions with chain D Water bridges: D:Q.79

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

PEG.5: 5 residues within 4Å: Chain A: E.32, G.34, K.74, T.76, V.99 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.74, A:T.76, A:T.76 PEG.15: 4 residues within 4Å: Chain B: G.2, V.3, Q.4, T.76 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.97 PEG.16: 3 residues within 4Å: Chain B: T.86, P.89, P.94 No protein-ligand interaction detected (PLIP) PEG.17: 4 residues within 4Å: Chain B: M.30, E.32, K.74, V.99 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.74 PEG.21: 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.29: 4 residues within 4Å: Chain C: A.40, A.44 Chain D: W.36, K.39 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.39 Water bridges: D:K.39 PEG.30: 3 residues within 4Å: Chain D: E.35, W.36, K.39 No protein-ligand interaction detected (PLIP)

2 x PE8: 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL(Non-covalent)

PE8.6: 9 residues within 4Å: Chain A: R.43, N.44, K.45, K.48, E.108 Chain D: E.59, M.62, F.63, A.66 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.45, A:K.48, A:E.108 PE8.18: 10 residues within 4Å: Chain B: D.80, A.82, Y.83, G.84, T.86, H.88 Chain D: E.59, V.60, F.63 Ligands: 60Z.7 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.87

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

PGE.19: 1 residues within 4Å: Chain B: A.85 No protein-ligand interaction detected (PLIP) PGE.25: 5 residues within 4Å: Chain A: Q.54 Chain C: F.63, A.66, S.67, E.70 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.71 PGE.31: 6 residues within 4Å: Chain A: R.19, K.53 Chain D: Q.75, Q.76, Q.79 Ligands: MG.26 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:K.53, D:Q.76, D:Q.79

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

PG4.22: 7 residues within 4Å: Chain A: T.86, H.88 Chain C: E.59, V.60, F.63 Ligands: 60Z.1, EDO.2 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Water bridges: C:E.59 Hydrogen bonds: A:A.82 PG4.23: 6 residues within 4Å: Chain B: K.36, F.37, D.38, I.91 Chain C: Q.58 Chain D: S.53 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: B:D.38, C:Q.58, D:S.53 PG4.24: 4 residues within 4Å: Chain C: R.27, A.31, I.34, E.35 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.35

1 x MG: MAGNESIUM ION(Non-covalent)

MG.26: 4 residues within 4Å: Chain A: K.53 Chain D: Q.76, Q.79 Ligands: PGE.31 No protein-ligand interaction detected (PLIP)

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
A

B
B

C
C

D
D

Peptidyl-prolyl cis-trans isomerase FKBP1A

Centrosome-associated protein CEP250

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