SMTL ID : 8dbj.1

Human PRPS1 with Phosphate, ATP, and R5P; Filament Interface

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

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

ATP.1: 12 residues within 4Å: Chain A: R.96, Q.97, K.99, H.130, D.171, G.173 Chain B: K.176 Chain F: F.35, N.37, E.39 Ligands: HSX.2, MG.4 14 PLIP interactions: 5 interactions with chain F, 1 interactions with chain B, 8 interactions with chain A Hydrogen bonds: F:N.37, F:N.37, F:E.39, A:Q.97, A:G.173 pi-Stacking: F:F.35, F:F.35 Salt bridges: B:K.176, A:K.99, A:K.99, A:H.130 Water bridges: A:K.99, A:K.99, A:K.99 ATP.6: 12 residues within 4Å: Chain A: K.176 Chain B: R.96, Q.97, K.99, H.130, D.171, G.173 Chain C: F.35, N.37, E.39 Ligands: HSX.7, MG.9 13 PLIP interactions: 1 interactions with chain A, 4 interactions with chain C, 8 interactions with chain B Salt bridges: A:K.176, B:K.99, B:K.99, B:H.130 Hydrogen bonds: C:N.37, C:N.37, B:Q.97, B:G.173 pi-Stacking: C:F.35, C:F.35 Water bridges: B:K.99, B:K.99, B:K.99 ATP.11: 12 residues within 4Å: Chain B: 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: 5 interactions with chain B, 8 interactions with chain C, 1 interactions with chain D Hydrogen bonds: B:N.37, B:N.37, B:E.39, C:Q.97, C:G.173 pi-Stacking: B:F.35, B:F.35 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 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: 8 interactions with chain D, 1 interactions with chain C, 4 interactions with chain E Hydrogen bonds: D:Q.97, D:G.173, E:N.37, E:N.37 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 pi-Stacking: E:F.35, E:F.35 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 A: 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: 8 interactions with chain F, 1 interactions with chain E, 4 interactions with chain A Hydrogen bonds: F:Q.97, F:G.173, A:N.37, A:N.37 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 pi-Stacking: A:F.35, A:F.35 ATP.31: 12 residues within 4Å: Chain G: R.96, Q.97, K.99, H.130, D.171, G.173 Chain H: K.176 Chain L: F.35, N.37, E.39 Ligands: HSX.32, MG.34 14 PLIP interactions: 8 interactions with chain G, 5 interactions with chain L, 1 interactions with chain H Hydrogen bonds: G:Q.97, G:G.173, L:N.37, L:N.37, L:E.39 Water bridges: G:K.99, G:K.99, G:K.99 Salt bridges: G:K.99, G:K.99, G:H.130, H:K.176 pi-Stacking: L:F.35, L:F.35 ATP.36: 12 residues within 4Å: Chain G: K.176 Chain H: R.96, Q.97, K.99, H.130, D.171, G.173 Chain I: F.35, N.37, E.39 Ligands: HSX.37, MG.39 13 PLIP interactions: 8 interactions with chain H, 1 interactions with chain G, 4 interactions with chain I Hydrogen bonds: H:Q.97, H:G.173, I:N.37, I:N.37 Water bridges: H:K.99, H:K.99, H:K.99 Salt bridges: H:K.99, H:K.99, H:H.130, G:K.176 pi-Stacking: I:F.35, I:F.35 ATP.41: 12 residues within 4Å: Chain H: F.35, N.37, E.39 Chain I: R.96, Q.97, K.99, H.130, D.171, G.173 Chain J: K.176 Ligands: HSX.42, MG.44 14 PLIP interactions: 5 interactions with chain H, 8 interactions with chain I, 1 interactions with chain J Hydrogen bonds: H:N.37, H:N.37, H:E.39, I:Q.97, I:G.173 pi-Stacking: H:F.35, H:F.35 Water bridges: I:K.99, I:K.99, I:K.99 Salt bridges: I:K.99, I:K.99, I:H.130, J:K.176 ATP.46: 12 residues within 4Å: Chain I: K.176 Chain J: R.96, Q.97, K.99, H.130, D.171, G.173 Chain K: F.35, N.37, E.39 Ligands: HSX.47, MG.49 13 PLIP interactions: 1 interactions with chain I, 8 interactions with chain J, 4 interactions with chain K Salt bridges: I:K.176, J:K.99, J:K.99, J:H.130 Hydrogen bonds: J:Q.97, J:G.173, K:N.37, K:N.37 Water bridges: J:K.99, J:K.99, J:K.99 pi-Stacking: K:F.35, K:F.35 ATP.51: 12 residues within 4Å: Chain J: F.35, N.37, E.39 Chain K: R.96, Q.97, K.99, H.130, D.171, G.173 Chain L: K.176 Ligands: HSX.52, MG.54 14 PLIP interactions: 5 interactions with chain J, 8 interactions with chain K, 1 interactions with chain L Hydrogen bonds: J:N.37, J:N.37, J:E.39, K:Q.97, K:G.173 pi-Stacking: J:F.35, J:F.35 Water bridges: K:K.99, K:K.99, K:K.99 Salt bridges: K:K.99, K:K.99, K:H.130, L:K.176 ATP.56: 12 residues within 4Å: Chain G: F.35, N.37, E.39 Chain K: K.176 Chain L: R.96, Q.97, K.99, H.130, D.171, G.173 Ligands: HSX.57, MG.59 13 PLIP interactions: 1 interactions with chain K, 4 interactions with chain G, 8 interactions with chain L Salt bridges: K:K.176, L:K.99, L:K.99, L:H.130 Hydrogen bonds: G:N.37, G:N.37, L:Q.97, L:G.173 pi-Stacking: G:F.35, G:F.35 Water bridges: L:K.99, L:K.99, L:K.99

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

HSX.2: 12 residues within 4Å: Chain A: H.130, D.171, D.220, D.221, M.222, D.224, T.225, C.226, G.227, T.228 Ligands: ATP.1, MG.5 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:H.130, A:D.224, A:D.224, A:D.224, A:T.225, A:C.226, A:G.227, A:T.228, A:T.228, A:T.228 Salt bridges: A:H.130 HSX.7: 12 residues within 4Å: Chain B: H.130, D.171, D.220, D.221, M.222, D.224, T.225, C.226, G.227, T.228 Ligands: ATP.6, MG.10 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:H.130, B:D.224, B:D.224, B:T.225, B:C.226, B:G.227, B:T.228, B:T.228, B:T.228 Salt bridges: B:H.130 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 HSX.32: 12 residues within 4Å: Chain G: H.130, D.171, D.220, D.221, M.222, D.224, T.225, C.226, G.227, T.228 Ligands: ATP.31, MG.35 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:H.130, G:D.224, G:D.224, G:D.224, G:T.225, G:C.226, G:G.227, G:T.228, G:T.228, G:T.228 Salt bridges: G:H.130 HSX.37: 12 residues within 4Å: Chain H: H.130, D.171, D.220, D.221, M.222, D.224, T.225, C.226, G.227, T.228 Ligands: ATP.36, MG.40 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:H.130, H:D.224, H:D.224, H:T.225, H:C.226, H:G.227, H:T.228, H:T.228, H:T.228 Salt bridges: H:H.130 HSX.42: 12 residues within 4Å: Chain I: H.130, D.171, D.220, D.221, M.222, D.224, T.225, C.226, G.227, T.228 Ligands: ATP.41, MG.45 11 PLIP interactions: 11 interactions with chain I Hydrogen bonds: I:H.130, I:D.224, I:D.224, I:D.224, I:T.225, I:C.226, I:G.227, I:T.228, I:T.228, I:T.228 Salt bridges: I:H.130 HSX.47: 12 residues within 4Å: Chain J: H.130, D.171, D.220, D.221, M.222, D.224, T.225, C.226, G.227, T.228 Ligands: ATP.46, MG.50 10 PLIP interactions: 10 interactions with chain J Hydrogen bonds: J:H.130, J:D.224, J:D.224, J:T.225, J:C.226, J:G.227, J:T.228, J:T.228, J:T.228 Salt bridges: J:H.130 HSX.52: 12 residues within 4Å: Chain K: H.130, D.171, D.220, D.221, M.222, D.224, T.225, C.226, G.227, T.228 Ligands: ATP.51, MG.55 11 PLIP interactions: 11 interactions with chain K Hydrogen bonds: K:H.130, K:D.224, K:D.224, K:D.224, K:T.225, K:C.226, K:G.227, K:T.228, K:T.228, K:T.228 Salt bridges: K:H.130 HSX.57: 12 residues within 4Å: Chain L: H.130, D.171, D.220, D.221, M.222, D.224, T.225, C.226, G.227, T.228 Ligands: ATP.56, MG.60 10 PLIP interactions: 10 interactions with chain L Hydrogen bonds: L:H.130, L:D.224, L:D.224, L:T.225, L:C.226, L:G.227, L:T.228, L:T.228, L:T.228 Salt bridges: L:H.130

12 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 C: S.47, R.49 6 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: A:S.308, A:S.308, A:V.309, A:S.310 Salt bridges: B:R.104, C:R.49 PO4.8: 6 residues within 4Å: Chain A: R.104 Chain B: S.308, V.309, S.310 Chain F: S.47, R.49 5 PLIP interactions: 1 interactions with chain F, 3 interactions with chain B, 1 interactions with chain A Salt bridges: F:R.49, A:R.104 Hydrogen bonds: B:V.309, B:S.310, B:S.310 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: 1 interactions with chain E, 4 interactions with chain C, 1 interactions with chain D Salt bridges: E:R.49, D:R.104 Hydrogen bonds: C:S.308, C:S.308, C:V.309, C:S.310 PO4.18: 6 residues within 4Å: Chain B: S.47, R.49 Chain C: R.104 Chain D: S.308, V.309, S.310 5 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D, 1 interactions with chain B Salt bridges: C:R.104, B:R.49 Hydrogen bonds: D:V.309, D:S.310, D:S.310 PO4.23: 6 residues within 4Å: Chain A: 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 A, 1 interactions with chain F Hydrogen bonds: E:S.308, E:S.308, E:V.309, E:S.310 Salt bridges: A: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 PO4.33: 6 residues within 4Å: Chain G: S.308, V.309, S.310 Chain H: R.104 Chain I: S.47, R.49 6 PLIP interactions: 1 interactions with chain H, 4 interactions with chain G, 1 interactions with chain I Salt bridges: H:R.104, I:R.49 Hydrogen bonds: G:S.308, G:S.308, G:V.309, G:S.310 PO4.38: 6 residues within 4Å: Chain G: R.104 Chain H: S.308, V.309, S.310 Chain L: S.47, R.49 5 PLIP interactions: 1 interactions with chain L, 3 interactions with chain H, 1 interactions with chain G Salt bridges: L:R.49, G:R.104 Hydrogen bonds: H:V.309, H:S.310, H:S.310 PO4.43: 6 residues within 4Å: Chain I: S.308, V.309, S.310 Chain J: R.104 Chain K: S.47, R.49 6 PLIP interactions: 1 interactions with chain K, 4 interactions with chain I, 1 interactions with chain J Salt bridges: K:R.49, J:R.104 Hydrogen bonds: I:S.308, I:S.308, I:V.309, I:S.310 PO4.48: 6 residues within 4Å: Chain H: S.47, R.49 Chain I: R.104 Chain J: S.308, V.309, S.310 5 PLIP interactions: 1 interactions with chain H, 3 interactions with chain J, 1 interactions with chain I Salt bridges: H:R.49, I:R.104 Hydrogen bonds: J:V.309, J:S.310, J:S.310 PO4.53: 6 residues within 4Å: Chain G: S.47, R.49 Chain K: S.308, V.309, S.310 Chain L: R.104 6 PLIP interactions: 1 interactions with chain L, 4 interactions with chain K, 1 interactions with chain G Salt bridges: L:R.104, G:R.49 Hydrogen bonds: K:S.308, K:S.308, K:V.309, K:S.310 PO4.58: 6 residues within 4Å: Chain J: S.47, R.49 Chain K: R.104 Chain L: S.308, V.309, S.310 5 PLIP interactions: 1 interactions with chain K, 3 interactions with chain L, 1 interactions with chain J Salt bridges: K:R.104, J:R.49 Hydrogen bonds: L:V.309, L:S.310, L:S.310

24 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: K.99, 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: 3 residues within 4Å: Chain A: D.171, D.220 Ligands: HSX.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.171 MG.9: 3 residues within 4Å: Chain B: K.99, H.130 Ligands: ATP.6 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.130, H2O.1, H2O.1 MG.10: 3 residues within 4Å: Chain B: D.171, D.220 Ligands: HSX.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: 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 MG.34: 3 residues within 4Å: Chain G: K.99, H.130 Ligands: ATP.31 3 PLIP interactions: 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:H.130, H2O.1, H2O.1 MG.35: 3 residues within 4Å: Chain G: D.171, D.220 Ligands: HSX.32 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.171 MG.39: 3 residues within 4Å: Chain H: K.99, H.130 Ligands: ATP.36 3 PLIP interactions: 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:H.130, H2O.1, H2O.1 MG.40: 3 residues within 4Å: Chain H: D.171, D.220 Ligands: HSX.37 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.171 MG.44: 3 residues within 4Å: Chain I: K.99, H.130 Ligands: ATP.41 3 PLIP interactions: 1 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:H.130, H2O.1, H2O.1 MG.45: 3 residues within 4Å: Chain I: D.171, D.220 Ligands: HSX.42 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:D.171 MG.49: 3 residues within 4Å: Chain J: K.99, H.130 Ligands: ATP.46 3 PLIP interactions: 1 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:H.130, H2O.1, H2O.1 MG.50: 3 residues within 4Å: Chain J: D.171, D.220 Ligands: HSX.47 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.171 MG.54: 3 residues within 4Å: Chain K: K.99, H.130 Ligands: ATP.51 3 PLIP interactions: 1 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:H.130, H2O.1, H2O.1 MG.55: 3 residues within 4Å: Chain K: D.171, D.220 Ligands: HSX.52 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.171 MG.59: 3 residues within 4Å: Chain L: K.99, H.130 Ligands: ATP.56 3 PLIP interactions: 1 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:H.130, H2O.1, H2O.1 MG.60: 3 residues within 4Å: Chain L: D.171, D.220 Ligands: HSX.57 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:D.171

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: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

Ribose-phosphate pyrophosphokinase 1

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