SMTL ID : 6vwp.2 (1 other biounit)

Crystal structure of E. coli guanosine kinase in complex with ppGpp

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.45 Å

Oligo State

homo-tetramer

Ligands

4 x G4P: GUANOSINE-5',3'-TETRAPHOSPHATE(Non-covalent)

G4P.1: 17 residues within 4Å: Chain A: R.10, S.12, K.13, H.14, R.305, Q.308, H.309, F.324, R.326, K.386, Y.394, S.396, A.398, Q.399, K.402 Chain B: D.436, R.437 19 PLIP interactions: 17 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.13, A:H.14, A:Y.394, A:Y.394, A:S.396, A:Q.399, A:K.402, B:R.437, B:R.437 Salt bridges: A:R.10, A:K.13, A:K.13, A:H.14, A:H.14, A:R.305, A:K.386, A:K.386 pi-Stacking: A:F.324, A:F.324 G4P.7: 16 residues within 4Å: Chain A: D.436, R.437 Chain B: R.10, S.12, K.13, H.14, R.305, Q.308, H.309, F.324, K.386, Y.394, S.396, A.398, Q.399, K.402 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.13, B:H.14, B:S.396, B:Q.399, B:K.402, A:R.437, A:R.437 Salt bridges: B:R.10, B:K.13, B:K.13, B:H.14, B:H.14, B:R.305, B:R.305, B:K.386, B:K.386 pi-Stacking: B:F.324, B:F.324 G4P.12: 18 residues within 4Å: Chain C: R.10, S.12, K.13, H.14, R.305, Q.308, H.309, F.324, R.326, K.386, Y.394, S.395, S.396, A.398, Q.399, K.402 Chain D: D.436, R.437 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:K.13, C:H.14, C:Y.394, C:Y.394, C:S.396, C:Q.399, C:K.402, D:R.437, D:R.437 Salt bridges: C:R.10, C:K.13, C:H.14, C:R.305, C:K.386, C:K.386 pi-Stacking: C:F.324, C:F.324 G4P.18: 19 residues within 4Å: Chain C: D.436, R.437 Chain D: F.6, R.10, K.11, S.12, K.13, H.14, R.305, Q.308, H.309, F.324, K.386, Y.394, S.395, S.396, A.398, Q.399, K.402 16 PLIP interactions: 14 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:K.13, D:R.305, D:Q.308, D:Y.394, D:Q.399, D:Q.399, C:R.437, C:R.437 Salt bridges: D:R.10, D:K.13, D:H.14, D:R.305, D:K.386, D:K.386 pi-Stacking: D:F.324, D:F.324

8 x GMP: GUANOSINE(Non-covalent)

GMP.2: 22 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, R.201, N.357, G.358, D.361, P.417 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.44, A:Q.44, A:D.48, A:G.96, A:T.97, A:T.97, A:N.100, A:R.201 Salt bridges: A:D.43 pi-Stacking: A:Y.198 GMP.3: 9 residues within 4Å: Chain A: L.278, D.279, W.280, V.281, D.282, F.298, H.330, K.331, R.338 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:L.278, A:L.278, A:D.282, A:R.338 pi-Stacking: A:H.330, A:H.330 pi-Cation interactions: A:H.330 GMP.8: 21 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, F.167, I.169, M.174, T.196, Y.198, R.201, N.357, G.358, D.361, P.417 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Q.44, B:Q.44, B:G.96, B:T.97, B:T.97, B:N.100, B:N.100, B:R.201 Salt bridges: B:D.43 GMP.9: 10 residues within 4Å: Chain B: L.278, D.279, W.280, V.281, D.282, F.298, H.330, K.331, R.338 Ligands: K.10 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 GMP.13: 24 residues within 4Å: Chain C: D.43, Q.44, L.46, D.48, S.68, G.95, G.96, T.97, I.98, N.100, C.155, T.157, R.165, F.167, I.169, M.174, T.196, Y.198, R.201, N.357, G.358, D.361, P.417 Ligands: MG.17 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:Q.44, C:Q.44, C:D.48, C:G.96, C:T.97, C:T.97, C:N.100, C:R.201, C:R.201, C:D.361 Salt bridges: C:D.43 pi-Stacking: C:F.167 GMP.14: 8 residues within 4Å: Chain C: L.278, D.279, W.280, V.281, D.282, F.298, H.330, R.338 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:L.278, C:V.281, C:D.282, C:H.330, C:R.338 pi-Stacking: C:H.330, C:H.330 pi-Cation interactions: C:H.330 GMP.19: 22 residues within 4Å: Chain D: D.43, Q.44, L.46, D.48, S.68, G.95, G.96, T.97, I.98, N.100, C.155, R.165, F.167, I.169, M.174, T.196, Y.198, L.199, R.201, G.358, D.361, P.417 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:Q.44, D:Q.44, D:G.96, D:T.97, D:N.100, D:N.100, D:R.201, D:G.358 Salt bridges: D:D.43 pi-Stacking: D:F.167, D:Y.198 GMP.20: 9 residues within 4Å: Chain D: L.278, D.279, W.280, V.281, D.282, F.298, H.330, R.338 Ligands: K.21 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:L.278, D:V.281, D:R.338 Salt bridges: D:D.282 pi-Stacking: D:H.330, D:H.330 pi-Cation interactions: D:H.330

6 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

K.4: 7 residues within 4Å: Chain A: L.133, C.134, N.135, T.136 Chain B: L.133, C.134, T.136 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:L.133, A:T.136, B:L.133, B:T.136 K.5: 6 residues within 4Å: Chain A: L.247, K.248, V.251, S.252, W.280, V.281 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:K.248, A:V.251, A:W.280 K.10: 6 residues within 4Å: Chain B: L.247, K.248, V.251, W.280, V.281 Ligands: GMP.9 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:K.248 K.15: 6 residues within 4Å: Chain C: L.133, C.134, T.136 Chain D: L.133, C.134, T.136 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Metal complexes: C:L.133, C:T.136, D:L.133, D:T.136 K.16: 6 residues within 4Å: Chain C: L.247, K.248, V.251, S.252, W.280, V.281 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:K.248, C:V.251, C:W.280 K.21: 3 residues within 4Å: Chain D: R.329, K.331 Ligands: GMP.20 No protein-ligand interaction detected (PLIP)

4 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain A: T.229, L.230, E.260, D.361 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.229 MG.11: 5 residues within 4Å: Chain B: T.97, T.229, L.230, E.260, D.361 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.229, B:L.230, B:D.361 MG.17: 6 residues within 4Å: Chain C: Y.198, L.230, G.231, E.260, D.361 Ligands: GMP.13 No protein-ligand interaction detected (PLIP) MG.22: 4 residues within 4Å: Chain D: T.229, L.230, E.260, D.361 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.229

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

D
F

Inosine-guanosine kinase

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