SMTL ID : 6zje.1

Crystal structure of human adenylate kinase 3, AK3, in complex with inhibitor Ap5A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

monomer

Ligands

1 x AP5: BIS(ADENOSINE)-5'-PENTAPHOSPHATE(Non-covalent)

AP5.1: 22 residues within 4Å: Chain A: P.16, G.17, G.19, G.21, T.22, 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.124, L.125, T.201 Ligands: CL.2, MG.5 33 PLIP interactions: 33 interactions with chain A Hydrogen bonds: A:G.17, A:T.22, A:S.38, A:G.39, A:I.66, A:R.94, A:Q.98, A:Q.98, A:T.201 Water bridges: A:K.20, A:K.20, A:G.21, A:G.21, A:T.22, A:T.22, A:S.37, A:S.37, A:R.43, A:R.43, A:K.64, A:D.90, A:R.94, A:R.94, A:N.139, A:N.139, A:R.172, A:R.172, A:R.172, A:R.172 Salt bridges: A:R.43, A:R.43 pi-Cation interactions: A:R.94, A:R.94

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

CL.2: 6 residues within 4Å: Chain A: G.17, S.18, G.19, K.20, G.21 Ligands: AP5.1 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: R.128, N.139 Ligand excluded by PLIP

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

NA.4: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.152

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

MG.5: 1 residues within 4Å: Ligands: AP5.1 No protein-ligand interaction detected (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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