SMTL ID : 6f7u.1

Molecular Mechanism of ATP versus GTP Selectivity of Adenylate Kinase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

2 x GCP: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Non-covalent)

GCP.1: 20 residues within 4Å: Chain A: A.8, P.9, G.10, A.11, G.12, K.13, G.14, R.119, I.120, R.123, D.158, R.167 Chain B: K.47, Q.48, D.51, I.52, D.54, A.55, K.57 Ligands: MG.2 23 PLIP interactions: 16 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:G.10, A:G.12, A:K.13, A:G.14, A:R.119, A:R.119, A:R.123, A:R.167 Water bridges: A:K.13, A:K.13, A:T.15, A:T.15, A:D.158, B:K.47, B:D.51, B:I.52, B:I.52, B:D.54 Salt bridges: A:R.123, A:D.158, B:K.47, B:D.51 pi-Cation interactions: A:R.167 GCP.3: 20 residues within 4Å: Chain A: K.47, Q.48, D.51, I.52, D.54, A.55, K.57 Chain B: A.8, P.9, G.10, A.11, G.12, K.13, G.14, R.119, I.120, R.123, D.158, R.167 Ligands: MG.4 23 PLIP interactions: 15 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:G.10, B:G.12, B:K.13, B:G.14, B:R.119, B:R.119, B:R.123, B:R.167 Water bridges: B:K.13, B:K.13, B:T.15, B:T.15, A:K.47, A:K.47, A:D.51, A:I.52, A:I.52, A:D.54 Salt bridges: B:R.123, B:D.158, A:K.47, A:D.51 pi-Cation interactions: B:R.167

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: K.13, G.14, Q.28, D.84 Ligands: GCP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.84 MG.4: 5 residues within 4Å: Chain B: K.13, G.14, Q.28, D.84 Ligands: GCP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rogne, P. et al., Molecular mechanism of ATP versus GTP selectivity of adenylate kinase. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-03-14

Peptides

Adenylate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Adenylate kinase

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