SMTL ID : 3mks.1 (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-2-2-mer

Ligands

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

SO4.1: 6 residues within 4Å: Chain B: F.20, L.24, K.51, S.52, T.53, S.54 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.53, B:S.54 SO4.2: 2 residues within 4Å: Chain B: P.19, F.20 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.20 SO4.3: 4 residues within 4Å: Chain B: Q.129, E.131, R.359, N.440 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.440 Water bridges: B:R.359, B:R.359 Salt bridges: B:R.359 SO4.4: 5 residues within 4Å: Chain B: V.425, H.426, A.427, N.428, I.429 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.427, B:N.428, B:I.429 Salt bridges: B:H.426 SO4.5: 7 residues within 4Å: Chain B: L.102, W.105, S.402, N.404, I.405, F.441, G.443 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.402, B:G.443 SO4.7: 5 residues within 4Å: Chain D: K.385, L.419, R.420, S.421, G.422 No protein-ligand interaction detected (PLIP) SO4.8: 6 residues within 4Å: Chain D: I.211, V.212, E.213, G.278, H.279, G.280 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.213, D:G.280 Salt bridges: D:H.279 SO4.9: 3 residues within 4Å: Chain D: R.207, R.225, Y.288 4 PLIP interactions: 4 interactions with chain D Water bridges: D:Y.288, D:Y.288 Salt bridges: D:R.207, D:R.225 SO4.10: 2 residues within 4Å: Chain D: Q.80, H.172 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.80, D:Q.80 Salt bridges: D:H.172 SO4.11: 2 residues within 4Å: Chain D: P.19, F.20 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:F.20 SO4.12: 5 residues within 4Å: Chain D: L.24, K.51, S.52, T.53, S.54 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.53, D:T.53, D:S.54

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

C1C.6: 12 residues within 4Å: Chain D: 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 D Hydrophobic interactions: D:L.354, D:A.369, D:R.375, D:W.377, D:R.384 Hydrogen bonds: D:G.350, D:W.377 Salt bridges: D:R.384, D:R.384 pi-Stacking: D:W.377 pi-Cation interactions: D:R.375, D:R.375, D:R.384

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 4 residues within 4Å: Chain D: Q.129, R.359, Y.400, N.440 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.359, D:R.359, D:Y.400, D:Y.400, D: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: AC
Cell division control protein 4: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Suppressor of kinetochore protein 1

Cell division control protein 4

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