SMTL ID : 3rgf.1

Crystal Structure of human CDK8/CycC

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-mer

Ligands

1 x BAX: 4-{4-[({[4-CHLORO-3-(TRIFLUOROMETHYL)PHENYL]AMINO}CARBONYL)AMINO]PHENOXY}-N-METHYLPYRIDINE-2-CARBOXAMIDE(Non-covalent)

BAX.1: 22 residues within 4Å: Chain A: V.37, A.52, K.54, E.68, L.72, L.75, V.80, I.81, F.99, D.100, Y.101, A.102, E.103, L.144, V.149, H.151, L.160, I.173, A.174, D.175, M.176, F.178 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:A.52, A:K.54, A:E.68, A:L.72, A:I.81, A:A.174, A:D.175, A:F.178 Hydrogen bonds: A:E.68, A:E.68, A:E.68, A:A.102, A:A.102, A:D.175 pi-Stacking: A:F.99 Halogen bonds: A:I.173

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

EDO.2: 6 residues within 4Å: Chain A: W.269, D.271, M.275, D.321, P.322, I.323 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.271, A:D.321 Water bridges: A:D.271 EDO.3: 5 residues within 4Å: Chain A: Y.135, Q.136, P.343, T.344, S.345 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.136 EDO.4: 5 residues within 4Å: Chain A: R.127, L.230, V.304, K.305, S.308 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.127, A:K.305, A:S.308 EDO.5: 4 residues within 4Å: Chain A: K.76, H.77, P.78, S.82 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.82, A:S.82 EDO.6: 6 residues within 4Å: Chain B: Q.43, T.47, T.68, F.71, K.72, Y.186 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.72 EDO.7: 7 residues within 4Å: Chain A: D.4, F.7 Chain B: K.29, Y.78, S.79, K.81, S.82 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.29, B:S.79, A:D.4, A:D.4, A:F.7 EDO.9: 6 residues within 4Å: Chain B: Q.51, G.54, E.55, L.59, Q.61, I.64 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.59, B:Q.61 EDO.10: 3 residues within 4Å: Chain B: Q.15, W.16, R.77 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.15, B:R.77 EDO.11: 2 residues within 4Å: Chain B: N.135, H.136 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.135 EDO.12: 4 residues within 4Å: Chain B: R.27, E.36, Y.39, W.40 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.36, B:W.40 EDO.13: 7 residues within 4Å: Chain B: A.2, A.4, Q.62, I.153, V.154, Y.155, R.159 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.1, B:Q.62, B:V.154, B:R.159

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 6 residues within 4Å: Chain B: I.44, N.48, R.187, W.243, F.246, E.248 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.48, B:R.187, B:R.187, B:F.246

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schneider, E.V. et al., The Structure of CDK8/CycC Implicates Specificity in the CDK/Cyclin Family and Reveals Interaction with a Deep Pocket Binder. J.Mol.Biol. (2011)

Release Date

2011-08-10

Peptides

Cyclin-dependent kinase 8: A
Cyclin-C: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cyclin-dependent kinase 8

Cyclin-C

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