SMTL ID : 1ao0.1

GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE (PRPP) AMIDOTRANSFERASE FROM B. SUBTILIS COMPLEXED WITH ADP AND GMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: S.283, D.345, D.346 Ligands: 5GP.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.283, A:D.345, A:D.346, H2O.1 MG.5: 5 residues within 4Å: Chain B: S.283, D.345, D.346 Ligands: 5GP.7, ADP.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.283, B:D.345, B:D.346, H2O.1 MG.9: 5 residues within 4Å: Chain C: S.283, D.345, D.346 Ligands: 5GP.11, ADP.12 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.283, C:D.345, C:D.346, H2O.1 MG.13: 5 residues within 4Å: Chain D: S.283, D.345, D.346 Ligands: 5GP.15, ADP.16 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:S.283, D:D.345, D:D.346, H2O.1

4 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.2: 9 residues within 4Å: Chain A: C.236, S.237, M.238, C.382, Y.384, T.388, C.437, A.439, C.440 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.236, A:C.382, A:C.437, A:C.440 SF4.6: 9 residues within 4Å: Chain B: C.236, S.237, M.238, C.382, Y.384, T.388, C.437, A.439, C.440 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.236, B:C.382, B:C.437, B:C.440 SF4.10: 9 residues within 4Å: Chain C: C.236, S.237, M.238, C.382, Y.384, T.388, C.437, A.439, C.440 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.236, C:C.382, C:C.437, C:C.440 SF4.14: 10 residues within 4Å: Chain D: L.177, C.236, S.237, M.238, C.382, Y.384, T.388, C.437, A.439, C.440 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.236, D:C.382, D:C.437, D:C.440

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

5GP.3: 14 residues within 4Å: Chain A: M.238, Y.242, S.283, D.345, D.346, S.347, V.349, R.350, G.351, T.352, T.353, D.387 Ligands: MG.1, ADP.4 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:S.283, A:D.346, A:S.347, A:S.347, A:S.347, A:S.347, A:V.349, A:R.350, A:G.351, A:T.352, A:T.353, A:T.353 Salt bridges: A:R.350 pi-Stacking: A:Y.242, A:Y.242 pi-Cation interactions: A:Y.242 5GP.7: 14 residues within 4Å: Chain B: M.238, Y.242, S.283, D.345, D.346, S.347, V.349, R.350, G.351, T.352, T.353, D.387 Ligands: MG.5, ADP.8 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:Y.242, B:S.283, B:D.346, B:S.347, B:S.347, B:S.347, B:S.347, B:V.349, B:R.350, B:G.351, B:T.352, B:T.353, B:T.353 Salt bridges: B:R.350 pi-Stacking: B:Y.242, B:Y.242 pi-Cation interactions: B:Y.242 5GP.11: 14 residues within 4Å: Chain C: M.238, Y.242, S.283, D.345, D.346, S.347, V.349, R.350, G.351, T.352, T.353, D.387 Ligands: MG.9, ADP.12 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:S.283, C:S.347, C:S.347, C:S.347, C:S.347, C:V.349, C:R.350, C:G.351, C:T.352, C:T.353, C:T.353 Salt bridges: C:R.350 pi-Stacking: C:Y.242, C:Y.242 pi-Cation interactions: C:Y.242 5GP.15: 16 residues within 4Å: Chain D: M.238, Y.242, S.283, D.345, D.346, S.347, I.348, V.349, R.350, G.351, T.352, T.353, I.378, D.387 Ligands: MG.13, ADP.16 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:Y.242, D:S.283, D:S.347, D:S.347, D:S.347, D:S.347, D:V.349, D:R.350, D:G.351, D:T.352, D:T.353, D:T.353 Salt bridges: D:D.346, D:R.350 pi-Stacking: D:Y.242, D:Y.242

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

ADP.4: 16 residues within 4Å: Chain A: H.25, Y.242, S.244, R.245, P.246, R.259, P.281, D.282, S.283, K.305, K.328 Chain B: I.304, K.305, N.306, R.307 Ligands: 5GP.3 16 PLIP interactions: 10 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:Y.242, A:Y.242, A:R.259, A:R.259, A:D.282, A:S.283, A:S.283, B:K.305, B:R.307, B:R.307, B:R.307 Salt bridges: A:K.305, A:K.328, A:K.328, B:R.307 pi-Cation interactions: B:R.307 ADP.8: 17 residues within 4Å: Chain A: I.304, K.305, N.306, R.307 Chain B: H.25, Y.242, S.244, R.245, P.246, R.259, P.281, D.282, S.283, K.305, K.328 Ligands: MG.5, 5GP.7 14 PLIP interactions: 5 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:K.305, A:R.307, A:R.307, B:Y.242, B:R.259, B:R.259, B:D.282, B:S.283, B:S.283 Salt bridges: A:R.307, B:K.305, B:K.328, B:K.328 pi-Cation interactions: A:R.307 ADP.12: 17 residues within 4Å: Chain C: H.25, Y.242, S.244, R.245, P.246, R.259, P.281, D.282, S.283, K.305, K.328 Chain D: I.304, K.305, N.306, R.307 Ligands: MG.9, 5GP.11 17 PLIP interactions: 11 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:Y.242, C:Y.242, C:R.259, C:R.259, C:D.282, C:S.283, C:S.283, D:K.305, D:R.307, D:R.307, D:R.307 Water bridges: C:S.283 Salt bridges: C:K.305, C:K.328, C:K.328, D:R.307 pi-Cation interactions: D:R.307 ADP.16: 15 residues within 4Å: Chain C: I.304, K.305, R.307 Chain D: H.25, Y.242, S.244, R.245, P.246, R.259, P.281, D.282, S.283, K.305 Ligands: MG.13, 5GP.15 16 PLIP interactions: 11 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:Y.242, D:R.259, D:R.259, D:D.282, D:S.283, D:S.283, C:K.305, C:R.307, C:R.307 Water bridges: D:S.283, D:D.346 Salt bridges: D:K.305, D:K.328, D:K.328, C:R.307 pi-Cation interactions: C:R.307

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, S. et al., Mechanism of the synergistic end-product regulation of Bacillus subtilis glutamine phosphoribosylpyrophosphate amidotransferase by nucleotides. Biochemistry (1997)

Release Date

1997-11-12

Peptides

GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE