SMTL ID : 9lo3.1

Transition state analogue(GMPK in complex with GMP, ADP, Mg2+ and AlF4- at 277 K)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: S.19 Ligands: ADP.3, ALF.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.19, H2O.1, H2O.2, H2O.5

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

5GP.2: 19 residues within 4Å: Chain A: G.12, K.18, S.38, R.42, R.45, Y.54, E.73, A.75, F.77, Y.82, G.83, T.84, D.102, V.103, D.104, G.107, R.149 Ligands: ADP.3, ALF.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.12, A:S.38, A:Y.54, A:T.84, A:D.102, A:D.104 Water bridges: A:R.42, A:R.45 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.3: 17 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, 5GP.2, ALF.4 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:G.15, A:A.16, A:G.17, A:K.18, A:S.19, A:T.20, A:T.20, A:N.172, A:D.173 Water bridges: A:T.20, A:R.45, A:R.45, A:R.134, A:R.134, A:R.134, A:R.134, A:R.138, A:L.175, A:L.175 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.4: 10 residues within 4Å: Chain A: S.14, G.15, K.18, S.19, R.45, R.138, R.149 Ligands: MG.1, 5GP.2, ADP.3 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: 5GP.2

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: E.28, H.29, S.30, G.31, I.32, Q.194 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.28, A:H.29, A:G.31 Water bridges: A:S.30 GOL.7: 4 residues within 4Å: Chain A: R.64, D.65, A.68, D.70 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.64, A:D.65, A:D.70 Water bridges: A:D.65, A:D.65

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.6: 6 residues within 4Å: Chain A: H.1, I.72, K.86, T.114, D.115, L.116 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.115 Water bridges: A:A.113, A:A.113, A:D.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, L. et al., Comprehensive profiling of the catalytic conformations of human Guanylate kinase. Nat Commun (2025)

Release Date

2025-09-10

Peptides

Guanylate kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Guanylate kinase

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