SMTL ID : 4f7s.1

Crystal structure of human CDK8/CYCC in the DMG-in conformation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 0SW: N-(2-phenylethyl)quinazolin-4-amine(Non-covalent)

0SW.1: 13 residues within 4Å: Chain A: V.29, A.52, I.81, F.99, D.100, Y.101, A.102, D.105, H.108, A.157, L.160, R.358 Ligands: EDO.7 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.52, A:I.81, A:F.99, A:A.157, A:L.160, A:L.160 Hydrogen bonds: A:A.102 Water bridges: A:D.175

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

EDO.2: 7 residues within 4Å: Chain A: R.73, E.74 Chain B: Q.11, S.12, S.13, L.16, Q.17 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.17, A:E.74 EDO.3: 8 residues within 4Å: Chain A: R.152, D.153, L.154, Y.201, L.206, I.217, D.218, A.221 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.152, A:L.154, A:Y.201, A:D.218 EDO.4: 4 residues within 4Å: Chain A: A.179, R.180, L.181, P.188 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.181 Water bridges: A:K.187 EDO.5: 3 residues within 4Å: Chain A: V.304, K.305, S.308 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.305, A:S.308 EDO.6: 4 residues within 4Å: Chain A: K.316, I.326, Q.330, D.334 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.316, A:D.334, A:D.334 EDO.7: 7 residues within 4Å: Chain A: K.54, E.68, I.81, F.99, A.174, D.175 Ligands: 0SW.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.175, A:D.175 EDO.8: 7 residues within 4Å: Chain B: D.2, A.4, M.5, A.6, I.155, V.156, R.161 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.2, B:R.161 EDO.9: 4 residues within 4Å: Chain B: F.9, W.10, P.198, F.199 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.199 EDO.10: 8 residues within 4Å: Chain B: Q.53, Q.63, A.67, T.70, Y.160, N.185, Y.188, R.189 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.63, B:Q.63, B:Y.160, B:R.189 EDO.11: 6 residues within 4Å: Chain B: I.46, N.50, R.189, W.245, F.248, E.250 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.50, B:R.189, B:E.250 EDO.12: 6 residues within 4Å: Chain B: Q.53, E.57, K.60, L.61, Q.63, I.66 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.53, B:Q.63 EDO.13: 4 residues within 4Å: Chain A: R.73, K.85, V.86 Chain B: D.151 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.86, A:V.86 EDO.14: 4 residues within 4Å: Chain B: R.62, Q.63, Q.64, W.181 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.63, B:Q.64

1 x FMT: FORMIC ACID(Non-functional Binders)

FMT.15: 6 residues within 4Å: Chain B: Q.45, T.49, T.70, F.73, K.74, Y.188 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.49, B:K.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schneider, E.V. et al., Structure-kinetic relationship study of CDK8/CycC specific compounds. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-05-01

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

Related Entries With Identical Sequence