SMTL ID : 4bgq.1

Crystal structure of the human CDKL5 kinase domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x NA: SODIUM ION(Non-functional Binders)

NA.1: 4 residues within 4Å: Chain A: V.93, E.94, S.145, H.146 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.94, A:H.146, A:H.146

1 x 38R: [4-({4-[(3-cyclopentyl-1H-pyrazol-5-yl)amino]pyrimidin-2-yl}amino)phenyl]acetonitrile(Non-covalent)

38R.2: 17 residues within 4Å: Chain A: V.20, Y.25, V.28, A.41, K.43, F.90, E.91, Y.92, V.93, E.94, K.95, N.96, E.99, E.140, L.143, C.153, D.154 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.20, A:V.28, A:A.41, A:F.90, A:L.143, A:D.154 Hydrogen bonds: A:V.93, A:V.93, A:V.93 pi-Stacking: A:Y.25

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

EDO.3: 2 residues within 4Å: Chain A: P.232, S.233 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.233 EDO.6: 1 residues within 4Å: Chain A: A.79 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.79 Water bridges: A:A.79

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 4 residues within 4Å: Chain A: A.284, D.285, R.286, Q.291 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.284, A:Q.291 Water bridges: A:L.288 ACT.5: 5 residues within 4Å: Chain A: H.125, H.128, K.129, K.191, T.289 3 PLIP interactions: 3 interactions with chain A Water bridges: A:H.128, A:T.289 Salt bridges: A:K.191

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Canning, P. et al., CDKL Family Kinases Have Evolved Distinct Structural Features and Ciliary Function. Cell Rep (2018)

Release Date

2013-05-08

Peptides

CYCLIN-DEPENDENT KINASE-LIKE 5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CYCLIN-DEPENDENT KINASE-LIKE 5

Related Entries With Identical Sequence