SMTL ID : 7xmv.1

E.coli phosphoribosylpyrophosphate (PRPP) synthetase type A(AMP/ADP) filament bound with ADP, AMP and R5P

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x HSX: 5-O-phosphono-alpha-D-ribofuranose(Non-covalent)

HSX.1: 11 residues within 4Å: Chain A: D.170, D.220, D.221, M.222, D.224, T.225, G.226, G.227, T.228 Ligands: MG.2, ADP.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.96, A:D.220, A:D.221, A:D.224, A:T.225, A:G.226, A:G.227, A:T.228, A:T.228, A:T.228 Water bridges: A:D.224, A:L.229, A:L.229 HSX.6: 11 residues within 4Å: Chain B: D.170, D.220, D.221, M.222, D.224, T.225, G.226, G.227, T.228 Ligands: MG.7, ADP.9 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:R.96, B:D.220, B:D.221, B:D.224, B:T.225, B:G.226, B:G.227, B:T.228, B:T.228, B:T.228 Water bridges: B:D.224, B:L.229, B:L.229 HSX.11: 11 residues within 4Å: Chain C: D.170, D.220, D.221, M.222, D.224, T.225, G.226, G.227, T.228 Ligands: MG.12, ADP.14 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:R.96, C:D.220, C:D.221, C:D.224, C:T.225, C:T.225, C:G.226, C:G.227, C:T.228 Water bridges: C:D.170, C:D.224, C:D.224, C:T.228, C:T.228, C:T.228, C:L.229 HSX.16: 11 residues within 4Å: Chain D: D.170, D.220, D.221, M.222, D.224, T.225, G.226, G.227, T.228 Ligands: MG.17, ADP.19 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:R.96, D:D.220, D:D.221, D:D.224, D:T.225, D:G.226, D:G.227, D:T.228, D:T.228, D:T.228 Water bridges: D:D.224, D:L.229 HSX.21: 11 residues within 4Å: Chain E: D.170, D.220, D.221, M.222, D.224, T.225, G.226, G.227, T.228 Ligands: MG.22, ADP.24 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:R.96, E:D.220, E:D.221, E:D.224, E:T.225, E:T.225, E:G.226, E:G.227, E:T.228 Water bridges: E:D.170, E:D.224, E:D.224, E:T.228, E:T.228, E:L.229, E:L.229 HSX.26: 11 residues within 4Å: Chain F: D.170, D.220, D.221, M.222, D.224, T.225, G.226, G.227, T.228 Ligands: MG.27, ADP.29 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:R.96, F:D.220, F:D.221, F:D.224, F:T.225, F:T.225, F:G.226, F:G.227, F:T.228 Water bridges: F:D.170, F:D.224, F:D.224, F:T.228, F:T.228, F:L.229

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.170, D.220 Ligands: HSX.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.170, H2O.1, H2O.1 MG.3: 2 residues within 4Å: Chain A: H.131 Ligands: ADP.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.131, H2O.1, H2O.1, H2O.1 MG.7: 3 residues within 4Å: Chain B: D.170, D.220 Ligands: HSX.6 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.170, H2O.6, H2O.6 MG.8: 2 residues within 4Å: Chain B: H.131 Ligands: ADP.9 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.131, H2O.6, H2O.6, H2O.6 MG.12: 3 residues within 4Å: Chain C: D.170, D.220 Ligands: HSX.11 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.170, H2O.11, H2O.11 MG.13: 2 residues within 4Å: Chain C: H.131 Ligands: ADP.14 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:H.131, H2O.11, H2O.12, H2O.12 MG.17: 3 residues within 4Å: Chain D: D.170, D.220 Ligands: HSX.16 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.170, H2O.16, H2O.17 MG.18: 2 residues within 4Å: Chain D: H.131 Ligands: ADP.19 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:H.131, H2O.16, H2O.17, H2O.17 MG.22: 3 residues within 4Å: Chain E: D.170, D.220 Ligands: HSX.21 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.170, H2O.21, H2O.22 MG.23: 2 residues within 4Å: Chain E: H.131 Ligands: ADP.24 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:H.131, H2O.22, H2O.22, H2O.22 MG.27: 3 residues within 4Å: Chain F: D.170, D.220 Ligands: HSX.26 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.170, H2O.27, H2O.27 MG.28: 2 residues within 4Å: Chain F: H.131 Ligands: ADP.29 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:H.131, H2O.27, H2O.27, H2O.27

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

ADP.4: 9 residues within 4Å: Chain A: R.96, Q.97, R.99, H.131 Chain F: F.35, D.37, E.39 Ligands: HSX.1, MG.3 18 PLIP interactions: 14 interactions with chain A, 4 interactions with chain F Hydrogen bonds: A:Q.97, F:D.37 Water bridges: A:R.96, A:Q.97, A:Q.97, A:R.99, A:R.99, A:R.99, A:R.99, A:R.99, A:H.131, A:H.131, F:D.37 Salt bridges: A:R.99, A:H.131 pi-Cation interactions: A:R.96 pi-Stacking: F:F.35, F:F.35 ADP.9: 9 residues within 4Å: Chain B: R.96, Q.97, R.99, H.131 Chain E: F.35, D.37, E.39 Ligands: HSX.6, MG.8 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain E Hydrogen bonds: B:Q.97, E:D.37 Water bridges: B:R.96, B:Q.97, B:Q.97, B:R.99, B:R.99, B:R.99, B:R.99, B:H.131, B:H.131, E:D.37 Salt bridges: B:R.99, B:H.131 pi-Cation interactions: B:R.96 pi-Stacking: E:F.35, E:F.35 ADP.14: 9 residues within 4Å: Chain C: R.96, Q.97, R.99, H.131 Chain D: F.35, D.37, E.39 Ligands: HSX.11, MG.13 21 PLIP interactions: 17 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:Q.97, C:D.224, D:D.37 Water bridges: C:R.96, C:Q.97, C:Q.97, C:Q.97, C:R.99, C:R.99, C:R.99, C:R.99, C:R.99, C:D.170, C:D.170, C:D.170, D:D.37 Salt bridges: C:R.99, C:H.131 pi-Cation interactions: C:R.96 pi-Stacking: D:F.35, D:F.35 ADP.19: 9 residues within 4Å: Chain C: F.35, D.37, E.39 Chain D: R.96, Q.97, R.99, H.131 Ligands: HSX.16, MG.18 18 PLIP interactions: 14 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:Q.97, C:D.37 Water bridges: D:R.96, D:Q.97, D:Q.97, D:R.99, D:R.99, D:R.99, D:R.99, D:R.99, D:H.131, D:H.131, C:D.37 Salt bridges: D:R.99, D:H.131 pi-Cation interactions: D:R.96 pi-Stacking: C:F.35, C:F.35 ADP.24: 9 residues within 4Å: Chain B: F.35, D.37, E.39 Chain E: R.96, Q.97, R.99, H.131 Ligands: HSX.21, MG.23 18 PLIP interactions: 14 interactions with chain E, 4 interactions with chain B Hydrogen bonds: E:Q.97, E:D.224, B:D.37 Water bridges: E:R.96, E:Q.97, E:Q.97, E:R.99, E:R.99, E:R.99, E:R.99, E:D.170, E:D.170, B:D.37 Salt bridges: E:R.99, E:H.131 pi-Cation interactions: E:R.96 pi-Stacking: B:F.35, B:F.35 ADP.29: 9 residues within 4Å: Chain A: F.35, D.37, E.39 Chain F: R.96, Q.97, R.99, H.131 Ligands: HSX.26, MG.28 19 PLIP interactions: 15 interactions with chain F, 4 interactions with chain A Hydrogen bonds: F:Q.97, F:D.224, A:D.37 Water bridges: F:R.96, F:Q.97, F:Q.97, F:R.99, F:R.99, F:R.99, F:R.99, F:D.170, F:D.170, F:D.170, A:D.37 Salt bridges: F:R.99, F:H.131 pi-Cation interactions: F:R.96 pi-Stacking: A:F.35, A:F.35

6 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.5: 9 residues within 4Å: Chain A: E.133, F.147, S.149, V.175, A.179, K.182 Chain C: R.99, V.101, R.102 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:S.149, A:S.149, C:R.99, C:R.102 Water bridges: A:S.149, A:R.176, A:A.179, A:K.182 Salt bridges: A:K.182, C:R.102 pi-Stacking: A:F.147, A:F.147 AMP.10: 9 residues within 4Å: Chain B: E.133, F.147, S.149, V.175, A.179, K.182 Chain F: R.99, V.101, R.102 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain F Hydrogen bonds: B:S.149, B:S.149, F:R.99, F:R.102 Water bridges: B:S.149, B:A.179, B:K.182 Salt bridges: B:K.182, F:R.102 pi-Stacking: B:F.147, B:F.147 AMP.15: 9 residues within 4Å: Chain A: R.99, V.101, R.102 Chain C: E.133, F.147, S.149, V.175, A.179, K.182 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:S.149, C:S.149, A:R.99, A:R.102 Water bridges: C:S.149, C:A.179, C:K.182 Salt bridges: C:K.182, A:R.102 pi-Stacking: C:F.147, C:F.147 AMP.20: 9 residues within 4Å: Chain D: E.133, F.147, S.149, V.175, A.179, K.182 Chain E: R.99, V.101, R.102 12 PLIP interactions: 9 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:S.149, D:S.149, E:R.99, E:R.102 Water bridges: D:S.149, D:R.176, D:A.179, D:K.182 Salt bridges: D:K.182, E:R.102 pi-Stacking: D:F.147, D:F.147 AMP.25: 9 residues within 4Å: Chain D: R.99, V.101, R.102 Chain E: E.133, F.147, S.149, V.175, A.179, K.182 11 PLIP interactions: 3 interactions with chain D, 8 interactions with chain E Hydrogen bonds: D:R.99, D:R.102, E:S.149, E:S.149 Salt bridges: D:R.102, E:K.182 Water bridges: E:S.149, E:A.179, E:K.182 pi-Stacking: E:F.147, E:F.147 AMP.30: 9 residues within 4Å: Chain B: R.99, V.101, R.102 Chain F: E.133, F.147, S.149, V.175, A.179, K.182 11 PLIP interactions: 3 interactions with chain B, 8 interactions with chain F Hydrogen bonds: B:R.99, B:R.102, F:S.149, F:S.149 Salt bridges: B:R.102, F:K.182 Water bridges: F:S.149, F:A.179, F:K.182 pi-Stacking: F:F.147, F:F.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, H.H. et al., Filamentation modulates allosteric regulation of PRPS. Elife (2022)

Release Date

2022-06-29

Peptides

Ribose-phosphate pyrophosphokinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

C
C

D
D

E
B

F
F

Ribose-phosphate pyrophosphokinase

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