SMTL ID : 8dbk.1

Human PRPS1 with Phosphate, ATP, and R5P; Hexamer with resolved catalytic loops

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

5 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 12 residues within 4Å: Chain A: R.96, Q.97, K.99, H.130, G.173, D.224 Chain B: K.176 Chain C: F.35, N.37, E.39 Ligands: HSX.2, MG.4 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:Q.97, A:G.173, C:N.37, C:N.37 Water bridges: A:K.99 Salt bridges: A:K.99, A:K.99, A:H.130 pi-Stacking: C:F.35, C:F.35 ATP.11: 12 residues within 4Å: Chain A: F.35, N.37, E.39 Chain C: R.96, Q.97, K.99, H.130, D.171, G.173 Chain D: K.176 Ligands: HSX.12, MG.14 14 PLIP interactions: 8 interactions with chain C, 5 interactions with chain A, 1 interactions with chain D Hydrogen bonds: C:Q.97, C:G.173, A:N.37, A:E.39, A:E.39 Water bridges: C:K.99, C:K.99, C:K.99 Salt bridges: C:K.99, C:K.99, C:H.130, D:K.176 pi-Stacking: A:F.35, A:F.35 ATP.16: 12 residues within 4Å: Chain C: K.176 Chain D: R.96, Q.97, K.99, H.130, D.171, G.173 Chain E: F.35, N.37, E.39 Ligands: HSX.17, MG.19 13 PLIP interactions: 4 interactions with chain E, 8 interactions with chain D, 1 interactions with chain C Hydrogen bonds: E:N.37, E:N.37, D:Q.97, D:G.173 pi-Stacking: E:F.35, E:F.35 Water bridges: D:K.99, D:K.99, D:K.99 Salt bridges: D:K.99, D:K.99, D:H.130, C:K.176 ATP.21: 12 residues within 4Å: Chain D: F.35, N.37, E.39 Chain E: R.96, Q.97, K.99, H.130, D.171, G.173 Chain F: K.176 Ligands: HSX.22, MG.24 14 PLIP interactions: 5 interactions with chain D, 8 interactions with chain E, 1 interactions with chain F Hydrogen bonds: D:N.37, D:N.37, D:E.39, E:Q.97, E:G.173 pi-Stacking: D:F.35, D:F.35 Water bridges: E:K.99, E:K.99, E:K.99 Salt bridges: E:K.99, E:K.99, E:H.130, F:K.176 ATP.26: 12 residues within 4Å: Chain B: F.35, N.37, E.39 Chain E: K.176 Chain F: R.96, Q.97, K.99, H.130, D.171, G.173 Ligands: HSX.27, MG.29 13 PLIP interactions: 4 interactions with chain B, 8 interactions with chain F, 1 interactions with chain E Hydrogen bonds: B:N.37, B:E.39, F:Q.97, F:G.173 pi-Stacking: B:F.35, B:F.35 Water bridges: F:K.99, F:K.99, F:K.99 Salt bridges: F:K.99, F:K.99, F:H.130, E:K.176

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

HSX.2: 13 residues within 4Å: Chain A: H.130, D.171, D.220, D.221, M.222, A.223, D.224, T.225, C.226, G.227, T.228 Ligands: ATP.1, MG.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:H.130, A:D.221, A:D.224, A:T.225, A:C.226, A:G.227, A:T.228, A:T.228, A:T.228 HSX.12: 12 residues within 4Å: Chain C: H.130, D.171, D.220, D.221, M.222, D.224, T.225, C.226, G.227, T.228 Ligands: ATP.11, MG.15 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:H.130, C:D.224, C:D.224, C:D.224, C:T.225, C:C.226, C:G.227, C:T.228, C:T.228, C:T.228 Salt bridges: C:H.130 HSX.17: 12 residues within 4Å: Chain D: H.130, D.171, D.220, D.221, M.222, D.224, T.225, C.226, G.227, T.228 Ligands: ATP.16, MG.20 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:H.130, D:D.224, D:D.224, D:T.225, D:C.226, D:G.227, D:T.228, D:T.228, D:T.228 Salt bridges: D:H.130 HSX.22: 12 residues within 4Å: Chain E: H.130, D.171, D.220, D.221, M.222, D.224, T.225, C.226, G.227, T.228 Ligands: ATP.21, MG.25 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:H.130, E:D.224, E:D.224, E:D.224, E:T.225, E:C.226, E:G.227, E:T.228, E:T.228, E:T.228 Salt bridges: E:H.130 HSX.27: 12 residues within 4Å: Chain F: H.130, D.171, D.220, D.221, M.222, D.224, T.225, C.226, G.227, T.228 Ligands: ATP.26, MG.30 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:H.130, F:D.224, F:D.224, F:T.225, F:C.226, F:G.227, F:T.228, F:T.228, F:T.228 Salt bridges: F:H.130

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 6 residues within 4Å: Chain A: S.308, V.309, S.310 Chain B: R.104 Chain F: S.47, R.49 5 PLIP interactions: 1 interactions with chain F, 3 interactions with chain A, 1 interactions with chain B Salt bridges: F:R.49, B:R.104 Hydrogen bonds: A:V.309, A:S.310, A:S.310 PO4.8: 7 residues within 4Å: Chain A: R.104 Chain B: E.307, S.308, V.309, S.310 Chain C: S.47, R.49 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:E.307, B:V.309, B:S.310 Salt bridges: C:R.49, A:R.104 PO4.13: 6 residues within 4Å: Chain C: S.308, V.309, S.310 Chain D: R.104 Chain E: S.47, R.49 6 PLIP interactions: 4 interactions with chain C, 1 interactions with chain E, 1 interactions with chain D Hydrogen bonds: C:S.308, C:S.308, C:V.309, C:S.310 Salt bridges: E:R.49, D:R.104 PO4.18: 6 residues within 4Å: Chain A: S.47, R.49 Chain C: R.104 Chain D: S.308, V.309, S.310 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: D:V.309, D:S.310, D:S.310 Salt bridges: A:R.49, C:R.104 PO4.23: 6 residues within 4Å: Chain B: S.47, R.49 Chain E: S.308, V.309, S.310 Chain F: R.104 6 PLIP interactions: 4 interactions with chain E, 1 interactions with chain B, 1 interactions with chain F Hydrogen bonds: E:S.308, E:S.308, E:V.309, E:S.310 Salt bridges: B:R.49, F:R.104 PO4.28: 6 residues within 4Å: Chain D: S.47, R.49 Chain E: R.104 Chain F: S.308, V.309, S.310 5 PLIP interactions: 3 interactions with chain F, 1 interactions with chain D, 1 interactions with chain E Hydrogen bonds: F:V.309, F:S.310, F:S.310 Salt bridges: D:R.49, E:R.104

12 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 2 residues within 4Å: Chain A: H.130 Ligands: ATP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.130, H2O.1, H2O.1 MG.5: 2 residues within 4Å: Chain A: D.171 Ligands: HSX.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.171 MG.9: 3 residues within 4Å: Chain B: H.130 Ligands: PRP.6, AMP.7 4 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:H.130, H2O.1, H2O.1, AMP.7 MG.10: 4 residues within 4Å: Chain B: D.171, D.220, D.221 Ligands: PRP.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.171, B:D.171 MG.14: 3 residues within 4Å: Chain C: K.99, H.130 Ligands: ATP.11 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.130, H2O.1, H2O.1 MG.15: 3 residues within 4Å: Chain C: D.171, D.220 Ligands: HSX.12 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.171 MG.19: 3 residues within 4Å: Chain D: K.99, H.130 Ligands: ATP.16 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.130, H2O.1, H2O.1 MG.20: 3 residues within 4Å: Chain D: D.171, D.220 Ligands: HSX.17 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.171 MG.24: 3 residues within 4Å: Chain E: K.99, H.130 Ligands: ATP.21 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.130, H2O.1, H2O.1 MG.25: 3 residues within 4Å: Chain E: D.171, D.220 Ligands: HSX.22 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.171 MG.29: 3 residues within 4Å: Chain F: K.99, H.130 Ligands: ATP.26 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.130, H2O.1, H2O.1 MG.30: 3 residues within 4Å: Chain F: D.171, D.220 Ligands: HSX.27 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.171

1 x PRP: 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose(Non-covalent)

PRP.6: 18 residues within 4Å: Chain B: R.96, H.130, D.171, G.173, K.194, R.196, D.220, D.221, M.222, A.223, D.224, T.225, C.226, G.227, T.228 Ligands: AMP.7, MG.9, MG.10 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:A.172, B:G.173, B:K.194, B:D.220, B:D.224, B:T.225, B:C.226, B:G.227, B:T.228, B:T.228, B:T.228 Water bridges: B:D.98, B:H.130 Salt bridges: B:H.130, B:H.130, B:H.130, B:K.194, B:K.194, B:K.194, B:R.196, B:R.196, B:R.196

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.7: 11 residues within 4Å: Chain A: K.176 Chain B: R.96, Q.97, K.99, D.101, N.200 Chain F: F.35, N.37, E.39 Ligands: PRP.6, MG.9 10 PLIP interactions: 4 interactions with chain B, 5 interactions with chain F, 1 interactions with chain A Hydrogen bonds: B:Q.97, B:D.101, B:D.224, F:N.37, F:N.37, F:E.39 Salt bridges: B:K.99, A:K.176 pi-Stacking: F:F.35, F:F.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hvorecny, K.L. et al., Human PRPS1 filaments stabilize allosteric sites to regulate activity. Nat.Struct.Mol.Biol. (2023)

Release Date

2023-02-15

Peptides

Ribose-phosphate pyrophosphokinase 1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Ribose-phosphate pyrophosphokinase 1

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