SMTL ID : 6ac9.3 (3 other biounits)

Crystal structure of human Vaccinia-related kinase 1 (VRK1) in complex with AMP-PNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

monomer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: R.241, R.279, D.310 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.241, A:R.241, A:R.279, A:R.279, A:D.310, A:D.310 Water bridges: A:Y.213, A:N.234, A:N.234, A:Y.311

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.2: 11 residues within 4Å: Chain A: I.51, V.69, K.71, M.131, D.132, R.133, F.134, N.182, L.184, D.197 Ligands: MG.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.132, A:F.134, A:D.197 Water bridges: A:S.181 Salt bridges: A:K.71

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

SO4.3: 2 residues within 4Å: Chain A: Q.95, H.171 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.95 Salt bridges: A:K.98, A:H.171

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: R.148, H.258 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: K.71, D.197 Ligands: ANP.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ngow, Y.S. et al., Crystal structure of human vaccinia-related kinase 1 in complex with AMP-PNP, a non-hydrolyzable ATP analog. Protein Sci. (2019)

Release Date

2018-12-26

Peptides

Serine/threonine-protein kinase VRK1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Serine/threonine-protein kinase VRK1

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