SMTL ID : 8crg.1 (1 other biounit)

E. coli adenylate kinase in complex with two ADP molecules as a result of enzymatic AP4A hydrolysis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

monomer

Ligands

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

ADP.1: 24 residues within 4Å: Chain A: A.8, P.9, G.10, A.11, G.12, K.13, G.14, T.15, Q.16, R.119, I.120, R.123, R.124, V.132, Y.133, H.134, F.137, N.138, G.198, K.200, P.201, V.202, V.205 Ligands: ADP.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:G.10, A:A.11, A:G.12, A:K.13, A:G.14, A:T.15, A:T.15, A:R.119, A:Y.133, A:K.200 Water bridges: A:D.84, A:R.123, A:N.138, A:R.156 Salt bridges: A:K.13, A:R.123, A:R.123 pi-Cation interactions: A:R.119 ADP.2: 23 residues within 4Å: Chain A: P.9, G.10, K.13, T.31, G.32, L.35, R.36, I.52, M.53, K.57, L.58, V.59, V.64, G.85, F.86, P.87, R.88, Q.92, R.123, R.156, D.158, R.167 Ligands: ADP.1 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: A:G.10, A:T.31, A:K.57, A:K.57, A:V.59, A:R.88, A:R.88, A:Q.92, A:Q.92, A:R.167 Water bridges: A:K.13, A:G.14, A:G.32, A:G.32, A:R.36, A:D.84, A:R.88, A:R.88, A:R.88, A:R.156 Salt bridges: A:K.13, A:R.36, A:R.88, A:R.88, A:R.123, A:R.156, A:R.156, A:R.167 pi-Cation interactions: A:R.88

1 x MPO: 3[N-MORPHOLINO]PROPANE SULFONIC ACID(Non-covalent)

MPO.3: 9 residues within 4Å: Chain A: I.65, V.68, K.69, I.72, F.86, A.95, M.96, A.99, I.101 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.69, A:A.99 Water bridges: A:K.69 Salt bridges: A:K.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tischlik, S. et al., Insights into Enzymatic Catalysis from Binding and Hydrolysis of Diadenosine Tetraphosphate by E. coli Adenylate Kinase. Biochemistry (2023)

Release Date

2023-06-14

Peptides

Adenylate kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Adenylate kinase

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