SMTL ID : 9jab.1 (1 other biounit)

Transition State Mimic(GMPK in complex with ADP, GMP , Mg2+, K+ and AlF4-)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: S.19, D.102 Ligands: 5GP.3, ADP.4, ALF.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.19

1 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: F.35, S.36, S.38, Y.54, D.102 Ligands: 5GP.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.38, A:D.102

1 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

5GP.3: 19 residues within 4Å: Chain A: S.14, K.18, S.38, R.42, R.45, Y.54, E.73, F.77, Y.82, G.83, T.84, D.102, V.103, D.104, G.107, R.149 Ligands: MG.1, K.2, ALF.5 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.14, A:K.18, A:K.18, A:Y.54, A:T.84, A:D.104 Salt bridges: A:R.42, A:R.45, A:E.73, A:D.104, A:R.149

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

ADP.4: 16 residues within 4Å: Chain A: P.13, S.14, G.15, A.16, G.17, K.18, S.19, T.20, R.134, R.138, N.172, D.173, S.174, L.175 Ligands: MG.1, ALF.5 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.15, A:A.16, A:G.17, A:K.18, A:S.19, A:S.19, A:T.20, A:N.172, A:D.173 Salt bridges: A:K.18, A:R.138, A:R.138 pi-Cation interactions: A:R.134

1 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.5: 10 residues within 4Å: Chain A: S.14, G.15, K.18, S.19, R.45, R.138, R.149 Ligands: MG.1, 5GP.3, ADP.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, L. et al., Comprehensive profiling of the catalytic conformations of human Guanylate kinase. To Be Published

Release Date

2025-09-03

Peptides

Guanylate kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Guanylate kinase

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