SMTL ID : 6vwo.1

Crystal structure of E. coli guanosine kinase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: N.257, T.287, A.288, G.289, P.290, G.292, L.293, P.345, M.347, I.353, G.358, A.359, G.360, A.363, N.405, S.408, L.412 Ligands: MG.7 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.257, A:T.287, A:G.289, A:A.359, A:G.360, A:N.405 Water bridges: A:N.257, A:E.258, A:E.260, A:T.356, A:G.358, A:G.358, A:G.358 ADP.8: 18 residues within 4Å: Chain B: N.257, T.287, A.288, G.289, P.290, G.292, L.293, P.345, M.347, I.353, G.358, A.359, G.360, A.363, N.405, S.408, L.412 Ligands: MG.14 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:N.257, B:T.287, B:G.289, B:A.359, B:G.360, B:N.405 Water bridges: B:N.257, B:E.258, B:E.260, B:T.356, B:G.358, B:G.358, B:G.358

4 x GMP: GUANOSINE(Non-covalent)

GMP.2: 23 residues within 4Å: Chain A: D.43, Q.44, L.46, D.48, S.68, G.95, G.96, T.97, I.98, N.100, C.155, T.157, F.167, I.169, M.174, T.196, Y.198, L.199, R.201, N.357, G.358, D.361, P.417 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Q.44, A:Q.44, A:D.48, A:G.96, A:T.97, A:N.100, A:R.201, A:D.361 Water bridges: A:Q.44, A:R.201, A:N.357 Salt bridges: A:D.43 pi-Stacking: A:Y.198, A:Y.198 GMP.3: 8 residues within 4Å: Chain A: L.278, D.279, W.280, V.281, D.282, F.298, H.330, R.338 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.278, A:V.281, A:R.338 pi-Stacking: A:H.330, A:H.330 pi-Cation interactions: A:H.330 GMP.9: 23 residues within 4Å: Chain B: D.43, Q.44, L.46, D.48, S.68, G.95, G.96, T.97, I.98, N.100, C.155, T.157, F.167, I.169, M.174, T.196, Y.198, L.199, R.201, N.357, G.358, D.361, P.417 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:Q.44, B:Q.44, B:D.48, B:G.96, B:T.97, B:N.100, B:R.201 Water bridges: B:Q.44, B:R.201, B:N.357 Salt bridges: B:D.43 pi-Stacking: B:Y.198, B:Y.198 GMP.10: 8 residues within 4Å: Chain B: L.278, D.279, W.280, V.281, D.282, F.298, H.330, R.338 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.278, B:V.281, B:R.338 pi-Stacking: B:H.330, B:H.330 pi-Cation interactions: B:H.330

6 x K: POTASSIUM ION(Non-covalent)

K.4: 7 residues within 4Å: Chain A: L.133, C.134, T.136 Chain B: L.133, C.134, T.136 Ligands: K.11 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Metal complexes: B:L.133, B:C.134, B:T.136, A:L.133, A:C.134, A:T.136 K.5: 5 residues within 4Å: Chain A: L.230, G.231, T.232, M.256, E.260 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:L.230, A:E.260, H2O.1, H2O.7, H2O.7 K.6: 7 residues within 4Å: Chain A: N.355, N.357, V.411, Q.414, H.415, S.416, P.417 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.355, A:N.357, A:V.411, A:Q.414, A:S.416 K.11: 7 residues within 4Å: Chain A: L.133, C.134, T.136 Chain B: L.133, C.134, T.136 Ligands: K.4 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Metal complexes: B:L.133, B:C.134, B:T.136, A:L.133, A:C.134, A:T.136 K.12: 5 residues within 4Å: Chain B: L.230, G.231, T.232, M.256, E.260 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:L.230, B:E.260, H2O.9, H2O.15, H2O.15 K.13: 7 residues within 4Å: Chain B: N.355, N.357, V.411, Q.414, H.415, S.416, P.417 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.355, B:N.357, B:V.411, B:Q.414, B:S.416

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.7: 2 residues within 4Å: Chain A: T.356 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain B: T.356 Ligands: ADP.8 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, B. et al., ppGpp Coordinates Nucleotide and Amino-Acid Synthesis in E. coli During Starvation. Mol.Cell (2020)

Release Date

2020-10-07

Peptides

Inosine-guanosine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Inosine-guanosine kinase

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