SMTL ID : 7xmu.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

HSX.1: 12 residues within 4Å: Chain A: H.131, D.170, D.220, D.221, M.222, D.224, T.225, G.226, G.227, T.228 Ligands: MG.2, ADP.5 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:H.131, A:D.220, A:D.224, A:T.225, A:G.226, A:G.227, A:T.228 Water bridges: A:R.96, A:L.229, A:L.229 HSX.8: 12 residues within 4Å: Chain B: H.131, D.170, D.220, D.221, M.222, D.224, T.225, G.226, G.227, T.228 Ligands: MG.9, ADP.12 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:H.131, B:D.220, B:D.224, B:T.225, B:G.226, B:G.227, B:T.228 Water bridges: B:R.96, B:L.229, B:L.229 HSX.14: 12 residues within 4Å: Chain C: H.131, D.170, D.220, D.221, M.222, D.224, T.225, G.226, G.227, T.228 Ligands: MG.15, ADP.18 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:H.131, C:D.220, C:D.224, C:D.224, C:D.224, C:T.225, C:T.225, C:G.226, C:G.227, C:T.228 Water bridges: C:R.96, C:R.96, C:D.170, C:L.229, C:L.229 HSX.20: 12 residues within 4Å: Chain D: H.131, D.170, D.220, D.221, M.222, D.224, T.225, G.226, G.227, T.228 Ligands: MG.21, ADP.24 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:H.131, D:D.220, D:D.224, D:T.225, D:G.226, D:G.227, D:T.228 Water bridges: D:R.96, D:R.96, D:L.229, D:L.229 HSX.26: 12 residues within 4Å: Chain E: H.131, D.170, D.220, D.221, M.222, D.224, T.225, G.226, G.227, T.228 Ligands: ADP.7, MG.27 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:H.131, E:D.220, E:D.224, E:D.224, E:D.224, E:T.225, E:T.225, E:G.226, E:G.227, E:T.228 Water bridges: E:R.96, E:R.96, E:D.170, E:L.229, E:L.229 HSX.31: 12 residues within 4Å: Chain F: H.131, D.170, D.220, D.221, M.222, D.224, T.225, G.226, G.227, T.228 Ligands: MG.32, ADP.35 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:H.131, F:D.220, F:D.224, F:D.224, F:D.224, F:T.225, F:T.225, F:G.226, F:G.227, F:T.228 Water bridges: F:R.96, F:D.170, F:L.229, F:L.229

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.170 Ligands: HSX.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.170, H2O.1, H2O.2 MG.4: 2 residues within 4Å: Chain A: H.131 Ligands: ADP.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.131, H2O.1, H2O.1, H2O.1 MG.9: 2 residues within 4Å: Chain B: D.170 Ligands: HSX.8 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.170, H2O.7, H2O.7 MG.11: 2 residues within 4Å: Chain B: H.131 Ligands: ADP.12 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.131, H2O.6, H2O.6, H2O.6 MG.15: 2 residues within 4Å: Chain C: D.170 Ligands: HSX.14 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.170, H2O.12, H2O.13 MG.17: 2 residues within 4Å: Chain C: H.131 Ligands: ADP.18 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:H.131, H2O.11, H2O.12, H2O.12 MG.21: 2 residues within 4Å: Chain D: D.170 Ligands: HSX.20 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.170, H2O.17, H2O.18 MG.23: 2 residues within 4Å: Chain D: H.131 Ligands: ADP.24 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:H.131, H2O.17, H2O.17, H2O.17 MG.27: 2 residues within 4Å: Chain E: D.170 Ligands: HSX.26 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.170, H2O.22, H2O.23 MG.29: 2 residues within 4Å: Chain E: H.131 Ligands: ADP.7 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:H.131, H2O.1, H2O.1, H2O.1 MG.32: 2 residues within 4Å: Chain F: D.170 Ligands: HSX.31 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.170, H2O.28, H2O.28 MG.34: 2 residues within 4Å: Chain F: H.131 Ligands: ADP.35 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 PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 9 residues within 4Å: Chain A: E.307, S.308, I.309, S.310 Chain B: N.47, R.49, A.80 Chain F: S.103, R.105 7 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B, 2 interactions with chain F Hydrogen bonds: A:I.309, A:S.310, B:N.47, B:N.47, F:S.103 Salt bridges: B:R.49, F:R.105 PO4.10: 9 residues within 4Å: Chain B: E.307, S.308, I.309, S.310 Chain C: S.103, R.105 Chain D: N.47, R.49, A.80 8 PLIP interactions: 2 interactions with chain B, 4 interactions with chain D, 2 interactions with chain C Hydrogen bonds: B:I.309, B:S.310, D:N.47, D:N.47, C:S.103 Water bridges: D:R.49 Salt bridges: D:R.49, C:R.105 PO4.16: 9 residues within 4Å: Chain B: S.103, R.105 Chain C: E.307, S.308, I.309, S.310 Chain F: N.47, R.49, A.80 7 PLIP interactions: 3 interactions with chain F, 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: F:N.47, F:A.80, C:I.309, C:S.310, B:S.103 Salt bridges: F:R.49, B:R.105 PO4.22: 9 residues within 4Å: Chain A: N.47, R.49, A.80 Chain D: E.307, S.308, I.309, S.310 Chain E: S.103, R.105 8 PLIP interactions: 2 interactions with chain D, 4 interactions with chain A, 2 interactions with chain E Hydrogen bonds: D:I.309, D:S.310, A:N.47, A:N.47, E:S.103 Water bridges: A:R.49 Salt bridges: A:R.49, E:R.105 PO4.28: 9 residues within 4Å: Chain C: N.47, R.49, A.80 Chain D: S.103, R.105 Chain E: E.307, S.308, I.309, S.310 8 PLIP interactions: 2 interactions with chain E, 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: E:I.309, E:S.310, C:N.47, C:A.80, D:S.103 Water bridges: C:R.49 Salt bridges: C:R.49, D:R.105 PO4.33: 9 residues within 4Å: Chain A: S.103, R.105 Chain E: N.47, R.49, A.80 Chain F: E.307, S.308, I.309, S.310 7 PLIP interactions: 2 interactions with chain F, 3 interactions with chain E, 2 interactions with chain A Hydrogen bonds: F:I.309, F:S.310, E:N.47, E:A.80, A:S.103 Salt bridges: E:R.49, A:R.105

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

ADP.5: 9 residues within 4Å: Chain A: R.96, Q.97, R.99, H.131 Chain E: F.35, D.37, E.39 Ligands: HSX.1, MG.4 14 PLIP interactions: 4 interactions with chain E, 10 interactions with chain A Hydrogen bonds: E:D.37, A:Q.97 Water bridges: E:S.36, A:R.96, A:Q.97, A:Q.97, A:Q.97, A:R.99, A:R.99, A:R.99 pi-Stacking: E:F.35, E:F.35 Salt bridges: A:R.99, A:H.131 ADP.6: 10 residues within 4Å: Chain A: E.133, F.147, S.149, V.175, R.178, A.179, K.182 Chain F: R.99, V.101, R.102 18 PLIP interactions: 3 interactions with chain F, 15 interactions with chain A Hydrogen bonds: F:R.99, F:R.102, A:S.149, A:S.149 Salt bridges: F:R.102, A:R.178, A:K.182, A:K.182 Water bridges: A:R.176, A:R.178, A:R.178, A:R.178, A:A.179, A:K.182, A:K.182, A:K.182 pi-Stacking: A:F.147, A:F.147 ADP.7: 9 residues within 4Å: Chain A: F.35, D.37, E.39 Chain E: R.96, Q.97, R.99, H.131 Ligands: HSX.26, MG.29 15 PLIP interactions: 4 interactions with chain A, 11 interactions with chain E Hydrogen bonds: A:D.37, E:Q.97 Water bridges: A:S.36, E:R.96, E:Q.97, E:Q.97, E:Q.97, E:R.99, E:R.99, E:R.99, E:H.131 pi-Stacking: A:F.35, A:F.35 Salt bridges: E:R.99, E:H.131 ADP.12: 9 residues within 4Å: Chain B: R.96, Q.97, R.99, H.131 Chain F: F.35, D.37, E.39 Ligands: HSX.8, MG.11 15 PLIP interactions: 10 interactions with chain B, 5 interactions with chain F Hydrogen bonds: B:Q.97, F:D.37 Water bridges: B:R.96, B:Q.97, B:Q.97, B:Q.97, B:R.99, B:R.99, B:R.99, F:S.36, F:S.36 Salt bridges: B:R.99, B:H.131 pi-Stacking: F:F.35, F:F.35 ADP.13: 10 residues within 4Å: Chain B: E.133, F.147, S.149, V.175, R.178, A.179, K.182 Chain C: R.99, V.101, R.102 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:S.149, B:S.149, C:R.99, C:R.102 Water bridges: B:R.176, B:R.178, B:R.178, B:R.178, B:A.179, B:K.182, B:K.182, B:K.182 Salt bridges: B:R.178, B:K.182, B:K.182, C:R.102 pi-Stacking: B:F.147, B:F.147 ADP.18: 9 residues within 4Å: Chain C: R.96, Q.97, R.99, H.131 Chain D: F.35, D.37, E.39 Ligands: HSX.14, MG.17 16 PLIP interactions: 11 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:Q.97, 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:H.131, D:S.36, D:S.36 Salt bridges: C:R.99, C:H.131 pi-Stacking: D:F.35, D:F.35 ADP.19: 10 residues within 4Å: Chain B: R.99, V.101, R.102 Chain C: E.133, F.147, S.149, V.175, R.178, A.179, K.182 18 PLIP interactions: 3 interactions with chain B, 15 interactions with chain C Hydrogen bonds: B:R.99, B:R.102, C:S.149, C:S.149 Salt bridges: B:R.102, C:R.178, C:K.182, C:K.182 Water bridges: C:R.176, C:R.178, C:R.178, C:R.178, C:A.179, C:K.182, C:K.182, C:K.182 pi-Stacking: C:F.147, C:F.147 ADP.24: 9 residues within 4Å: Chain C: F.35, D.37, E.39 Chain D: R.96, Q.97, R.99, H.131 Ligands: HSX.20, MG.23 15 PLIP interactions: 10 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:Q.97, C:D.37 Water bridges: D:R.96, D:Q.97, D:Q.97, D:Q.97, D:R.99, D:R.99, D:R.99, C:S.36, C:S.36 Salt bridges: D:R.99, D:H.131 pi-Stacking: C:F.35, C:F.35 ADP.25: 10 residues within 4Å: Chain D: E.133, F.147, S.149, V.175, R.178, A.179, K.182 Chain E: R.99, V.101, R.102 18 PLIP interactions: 15 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:R.176, D:R.178, D:R.178, D:R.178, D:A.179, D:K.182, D:K.182, D:K.182 Salt bridges: D:R.178, D:K.182, D:K.182, E:R.102 pi-Stacking: D:F.147, D:F.147 ADP.30: 10 residues within 4Å: Chain D: R.99, V.101, R.102 Chain E: E.133, F.147, S.149, V.175, R.178, A.179, K.182 18 PLIP interactions: 15 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:S.149, E:S.149, D:R.99, D:R.102 Water bridges: E:R.176, E:R.178, E:R.178, E:R.178, E:A.179, E:K.182, E:K.182, E:K.182 Salt bridges: E:R.178, E:K.182, E:K.182, D:R.102 pi-Stacking: E:F.147, E:F.147 ADP.35: 9 residues within 4Å: Chain B: F.35, D.37, E.39 Chain F: R.96, Q.97, R.99, H.131 Ligands: HSX.31, MG.34 16 PLIP interactions: 11 interactions with chain F, 5 interactions with chain B Hydrogen bonds: F:Q.97, B:D.37 Water bridges: F:R.96, F:Q.97, F:Q.97, F:Q.97, F:R.99, F:R.99, F:R.99, F:H.131, B:S.36, B:S.36 Salt bridges: F:R.99, F:H.131 pi-Stacking: B:F.35, B:F.35 ADP.36: 10 residues within 4Å: Chain A: R.99, V.101, R.102 Chain F: E.133, F.147, S.149, V.175, R.178, A.179, K.182 18 PLIP interactions: 15 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:S.149, F:S.149, A:R.99, A:R.102 Water bridges: F:R.176, F:R.178, F:R.178, F:R.178, F:A.179, F:K.182, F:K.182, F:K.182 Salt bridges: F:R.178, F:K.182, F:K.182, A:R.102 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
D

C
B

D
E

E
F

F
C

Ribose-phosphate pyrophosphokinase

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