SMTL ID : 8rj4.3 (3 other biounits)

E. coli adenylate kinase in complex with two ADP molecules and Mg2+ as a result of enzymatic AP4A hydrolysis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

monomer

Ligands

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

ADP.1: 20 residues within 4Å: Chain A: A.8, P.9, G.10, A.11, G.12, K.13, G.14, T.15, R.119, R.123, V.132, Y.133, H.134, F.137, N.138, G.198, K.200, P.201, V.202 Ligands: ADP.2 17 PLIP interactions: 17 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:R.119, A:N.138, A:K.200 Water bridges: A:D.84, A:R.119 Salt bridges: A:K.13, A:R.123, A:R.123 pi-Cation interactions: A:R.119 ADP.2: 19 residues within 4Å: Chain A: P.9, T.31, G.32, L.35, R.36, M.53, K.57, L.58, V.59, V.64, G.85, F.86, R.88, Q.92, R.123, R.156, D.158, R.167 Ligands: ADP.1 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:G.10, A:T.31, A:K.57, A:V.59, A:R.88, A:Q.92, A:Q.92, A:R.167, A:R.167 Water bridges: A:K.13, A:K.13, A:K.13, A:G.14, A:G.32, A:G.56, A:R.88, A:R.156, A:R.156, A:D.158 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 CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain A: G.46, K.47, Q.48 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nam, K. et al., Magnesium induced structural reorganization in the active site of adenylate kinase. Sci Adv (2024)

Release Date

2024-07-10

Peptides

Adenylate kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Adenylate kinase

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