SMTL ID : 4qrh.2 (1 other biounit)

Molecular mechanism and evolution of guanylate kinase regulation by (p)ppGpp

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: Y.81 Ligands: 0O2.4 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain B: Y.81 Ligands: 0O2.10 No protein-ligand interaction detected (PLIP)

2 x K: POTASSIUM ION(Non-covalent)

K.2: 4 residues within 4Å: Chain A: Y.39, S.42, E.106 Ligands: 0O2.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.39, A:S.42, A:E.106, H2O.1, H2O.1 K.6: 4 residues within 4Å: Chain B: Y.39, S.42, E.106 Ligands: 0O2.10 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:Y.39, B:S.42, B:E.106, H2O.7, H2O.8

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: R.46, Q.47, N.84 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.47, A:N.84, A:N.84 Water bridges: A:R.49, A:R.49

2 x 0O2: guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate)(Non-covalent)

0O2.4: 23 residues within 4Å: Chain A: P.17, S.18, G.19, V.20, G.21, K.22, G.23, S.42, R.46, R.49, Y.58, E.77, A.79, Y.81, Y.86, G.87, T.88, E.106, I.107, E.108, G.111 Ligands: MG.1, K.2 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:S.18, A:G.19, A:V.20, A:G.21, A:K.22, A:G.23, A:S.42, A:Y.58, A:Y.81, A:Y.81, A:T.88, A:E.106, A:E.106, A:E.108, A:G.111 Water bridges: A:G.21, A:Y.39, A:R.49, A:R.49 Salt bridges: A:K.22, A:K.22, A:R.46, A:R.49, A:R.49, A:R.49, A:E.77, A:E.108 0O2.10: 23 residues within 4Å: Chain B: P.17, S.18, G.19, V.20, G.21, K.22, G.23, S.42, R.46, R.49, Y.58, E.77, A.79, Y.81, Y.86, G.87, T.88, E.106, I.107, E.108, G.111 Ligands: MG.5, K.6 26 PLIP interactions: 26 interactions with chain B Hydrogen bonds: B:G.19, B:V.20, B:G.21, B:K.22, B:G.23, B:S.42, B:Y.58, B:Y.86, B:E.106, B:E.106, B:E.108, B:G.111 Water bridges: B:G.16, B:G.19, B:G.21, B:K.22, B:R.49, B:R.49 Salt bridges: B:K.22, B:K.22, B:R.46, B:R.49, B:R.49, B:R.49, B:E.77, B:E.108

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 1 residues within 4Å: Chain B: V.82 4 PLIP interactions: 4 interactions with chain B Water bridges: B:E.80, B:E.80, B:V.82, B:G.83 EDO.8: 6 residues within 4Å: Chain B: A.112, K.113, R.116, F.124, L.166, Y.167 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.116, B:L.166 Water bridges: B:V.109, B:K.113 EDO.9: 3 residues within 4Å: Chain B: R.46, Q.47, N.84 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.47, B:Q.47, B:Q.47, B:N.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, K. et al., Molecular Mechanism and Evolution of Guanylate Kinase Regulation by (p)ppGpp. Mol.Cell (2015)

Release Date

2015-02-25

Peptides

Guanylate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Guanylate kinase

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