SMTL ID : 3mks.3 (2 other biounits)

Crystal Structure of yeast Cdc4/Skp1 in complex with an allosteric inhibitor SCF-I2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-mer

Ligands

1 x C1C: 1,1'-binaphthalene-2,2'-dicarboxylic acid(Non-covalent)

C1C.1: 12 residues within 4Å: Chain B: L.348, Q.349, G.350, T.352, L.354, A.369, R.375, G.376, W.377, R.384, F.386, S.387 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.354, B:A.369, B:R.375, B:W.377, B:R.384 Hydrogen bonds: B:G.350, B:W.377 Salt bridges: B:R.384, B:R.384 pi-Stacking: B:W.377 pi-Cation interactions: B:R.375, B:R.375, B:R.384

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

SO4.2: 5 residues within 4Å: Chain B: K.385, L.419, R.420, S.421, G.422 No protein-ligand interaction detected (PLIP) SO4.3: 6 residues within 4Å: Chain B: I.211, V.212, E.213, G.278, H.279, G.280 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.213, B:G.280 Salt bridges: B:H.279 SO4.4: 3 residues within 4Å: Chain B: R.207, R.225, Y.288 4 PLIP interactions: 4 interactions with chain B Water bridges: B:Y.288, B:Y.288 Salt bridges: B:R.207, B:R.225 SO4.5: 2 residues within 4Å: Chain B: Q.80, H.172 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.80, B:Q.80 Salt bridges: B:H.172 SO4.6: 2 residues within 4Å: Chain B: P.19, F.20 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.20 SO4.7: 5 residues within 4Å: Chain B: L.24, K.51, S.52, T.53, S.54 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.53, B:T.53, B:S.54

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 4 residues within 4Å: Chain B: Q.129, R.359, Y.400, N.440 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.359, B:R.359, B:Y.400, B:Y.400, B:N.440

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Orlicky, S. et al., An allosteric inhibitor of substrate recognition by the SCF(Cdc4) ubiquitin ligase. Nat.Biotechnol. (2010)

Release Date

2010-07-21

Peptides

Suppressor of kinetochore protein 1: A
Cell division control protein 4: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Suppressor of kinetochore protein 1

Cell division control protein 4

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