SMTL ID : 6d3k.1 (1 other biounit)

Crystal structure of unphosphorylated human PKR kinase domain in complex with ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 19 residues within 4Å: Chain A: I.45, G.46, F.50, G.51, V.53, V.66, K.68, V.93, M.138, E.139, F.140, C.141, T.145, S.190, N.191, F.193, D.204 Ligands: PO4.2, MG.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.139, A:C.141, A:S.190, A:D.204 Salt bridges: A:K.68, A:K.68 ADP.5: 15 residues within 4Å: Chain B: G.46, S.47, G.51, V.53, V.66, K.68, M.138, E.139, C.141, T.145, S.190, N.191, F.193, D.204 Ligands: MG.7 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.51, B:E.139, B:C.141, B:D.204 Salt bridges: B:K.68, B:K.68 pi-Stacking: B:F.193, B:F.193

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 5 residues within 4Å: Chain A: K.188, S.190, N.191 Ligands: ADP.1, MG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.190 Salt bridges: A:K.188 PO4.6: 3 residues within 4Å: Chain B: K.188, S.190 Ligands: MG.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.190 Water bridges: B:E.147, B:S.190 Salt bridges: B:K.188

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: N.191, D.204 Ligands: ADP.1, PO4.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.204 MG.7: 4 residues within 4Å: Chain B: N.191, D.204 Ligands: ADP.5, PO4.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.204

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

SO4.4: 1 residues within 4Å: Chain A: K.143 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.143 SO4.8: 2 residues within 4Å: Chain B: R.306, K.313 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.306, B:K.313 SO4.9: 3 residues within 4Å: Chain B: K.282, P.315, E.316 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.316 Salt bridges: B:K.282 SO4.10: 3 residues within 4Å: Chain B: G.62, K.63, T.64 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.64, B:T.64 Salt bridges: B:K.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mayo, C.B. et al., Structural Basis of Protein Kinase R Autophosphorylation. Biochemistry (2019)

Release Date

2019-07-10

Peptides

Interferon-induced, double-stranded RNA-activated protein kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Interferon-induced, double-stranded RNA-activated protein kinase

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