SMTL ID : 6zjd.1

Crystal structure of human adenylate kinase 3, AK3, in complex with inhibitor ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 15 residues within 4Å: Chain A: P.16, S.38, G.39, L.42, R.43, I.60, K.64, L.65, I.66, M.71, G.91, R.94, Q.98, R.172 Ligands: MG.2 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:S.38, A:G.39, A:I.66, A:R.94, A:Q.98, A:Q.98 Water bridges: A:K.20, A:R.43, A:R.43, A:R.94, A:R.94, A:R.94, A:R.94, A:R.172, A:R.172, A:R.172, A:R.172 Salt bridges: A:R.43, A:R.94, A:R.172, A:R.172 pi-Cation interactions: A:R.94, A:R.94

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 1 residues within 4Å: Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

NA.4: 1 residues within 4Å: Chain A: D.40 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.40 Water bridges: A:S.37 NA.8: 1 residues within 4Å: Chain A: D.40 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.35

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

CL.5: 4 residues within 4Å: Chain A: E.32, L.33, K.34, Y.85 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain A: G.17, S.18, G.19, K.20, G.21 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: R.128, N.139 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rogne, P. et al., Structural Basis for GTP versus ATP Selectivity in the NMP Kinase AK3. Biochemistry (2020)

Release Date

2020-09-16

Peptides

GTP:AMP phosphotransferase AK3, mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTP:AMP phosphotransferase AK3, mitochondrial

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