SMTL ID : 8dbh.1

Human PRPS1 with Phosphate and ATP; 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: 11 residues within 4Å: Chain A: R.96, Q.97, K.99, H.130, G.173, D.224 Chain B: K.176 Chain F: F.35, N.37, E.39 Ligands: MG.4 12 PLIP interactions: 6 interactions with chain A, 5 interactions with chain F, 1 interactions with chain B Hydrogen bonds: A:Q.97, A:D.224, F:N.37, F:N.37, F:E.39 Water bridges: A:K.99 Salt bridges: A:K.99, A:K.99, A:H.130, B:K.176 pi-Stacking: F:F.35, F:F.35 ATP.6: 11 residues within 4Å: Chain A: K.176 Chain B: R.96, Q.97, K.99, H.130, G.173, D.224 Chain C: F.35, N.37, E.39 Ligands: MG.9 10 PLIP interactions: 5 interactions with chain B, 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:Q.97, C:N.37, C:N.37 Water bridges: B:K.99 Salt bridges: B:K.99, B:K.99, B:H.130, A:K.176 pi-Stacking: C:F.35, C:F.35 ATP.11: 11 residues within 4Å: Chain B: F.35, N.37, E.39 Chain C: R.96, Q.97, K.99, H.130, G.173, D.224 Chain D: K.176 Ligands: MG.14 12 PLIP interactions: 6 interactions with chain C, 5 interactions with chain B, 1 interactions with chain D Hydrogen bonds: C:Q.97, C:D.224, B:N.37, B:N.37, B:E.39 Water bridges: C:K.99 Salt bridges: C:K.99, C:K.99, C:H.130, D:K.176 pi-Stacking: B:F.35, B:F.35 ATP.16: 11 residues within 4Å: Chain C: K.176 Chain D: R.96, Q.97, K.99, H.130, G.173, D.224 Chain E: F.35, N.37, E.39 Ligands: MG.19 10 PLIP interactions: 5 interactions with chain D, 4 interactions with chain E, 1 interactions with chain C Hydrogen bonds: D:Q.97, E:N.37, E:N.37 Water bridges: 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: 11 residues within 4Å: Chain D: F.35, N.37, E.39 Chain E: R.96, Q.97, K.99, H.130, G.173, D.224 Chain F: K.176 Ligands: MG.24 12 PLIP interactions: 5 interactions with chain D, 6 interactions with chain E, 1 interactions with chain F Hydrogen bonds: D:N.37, D:N.37, D:E.39, E:Q.97, E:D.224 pi-Stacking: D:F.35, D:F.35 Water bridges: E:K.99 Salt bridges: E:K.99, E:K.99, E:H.130, F:K.176 ATP.26: 11 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, G.173, D.224 Ligands: MG.29 10 PLIP interactions: 5 interactions with chain F, 4 interactions with chain A, 1 interactions with chain E Hydrogen bonds: F:Q.97, A:N.37, A:N.37 Water bridges: 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: 11 residues within 4Å: Chain G: R.96, Q.97, K.99, H.130, G.173, D.224 Chain H: K.176 Chain L: F.35, N.37, E.39 Ligands: MG.34 12 PLIP interactions: 5 interactions with chain L, 6 interactions with chain G, 1 interactions with chain H Hydrogen bonds: L:N.37, L:N.37, L:E.39, G:Q.97, G:D.224 pi-Stacking: L:F.35, L:F.35 Water bridges: G:K.99 Salt bridges: G:K.99, G:K.99, G:H.130, H:K.176 ATP.36: 11 residues within 4Å: Chain G: K.176 Chain H: R.96, Q.97, K.99, H.130, G.173, D.224 Chain I: F.35, N.37, E.39 Ligands: MG.39 10 PLIP interactions: 4 interactions with chain I, 5 interactions with chain H, 1 interactions with chain G Hydrogen bonds: I:N.37, I:N.37, H:Q.97 pi-Stacking: I:F.35, I:F.35 Water bridges: H:K.99 Salt bridges: H:K.99, H:K.99, H:H.130, G:K.176 ATP.41: 11 residues within 4Å: Chain H: F.35, N.37, E.39 Chain I: R.96, Q.97, K.99, H.130, G.173, D.224 Chain J: K.176 Ligands: MG.44 12 PLIP interactions: 6 interactions with chain I, 5 interactions with chain H, 1 interactions with chain J Hydrogen bonds: I:Q.97, I:D.224, H:N.37, H:N.37, H:E.39 Water bridges: I:K.99 Salt bridges: I:K.99, I:K.99, I:H.130, J:K.176 pi-Stacking: H:F.35, H:F.35 ATP.46: 11 residues within 4Å: Chain I: K.176 Chain J: R.96, Q.97, K.99, H.130, G.173, D.224 Chain K: F.35, N.37, E.39 Ligands: MG.49 10 PLIP interactions: 1 interactions with chain I, 5 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, K:N.37, K:N.37 Water bridges: J:K.99 pi-Stacking: K:F.35, K:F.35 ATP.51: 11 residues within 4Å: Chain J: F.35, N.37, E.39 Chain K: R.96, Q.97, K.99, H.130, G.173, D.224 Chain L: K.176 Ligands: MG.54 12 PLIP interactions: 6 interactions with chain K, 5 interactions with chain J, 1 interactions with chain L Hydrogen bonds: K:Q.97, K:D.224, J:N.37, J:N.37, J:E.39 Water bridges: K:K.99 Salt bridges: K:K.99, K:K.99, K:H.130, L:K.176 pi-Stacking: J:F.35, J:F.35 ATP.56: 11 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, G.173, D.224 Ligands: MG.59 10 PLIP interactions: 1 interactions with chain K, 4 interactions with chain G, 5 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 pi-Stacking: G:F.35, G:F.35 Water bridges: L:K.99

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

PO4.2: 5 residues within 4Å: Chain A: D.224, T.225, C.226, G.227, T.228 Ligand excluded by PLIP PO4.3: 6 residues within 4Å: Chain A: S.308, V.309, S.310 Chain B: R.104 Chain C: S.47, R.49 Ligand excluded by PLIP PO4.7: 5 residues within 4Å: Chain B: D.224, T.225, C.226, G.227, T.228 Ligand excluded by PLIP PO4.8: 6 residues within 4Å: Chain A: R.104 Chain B: S.308, V.309, S.310 Chain F: S.47, R.49 Ligand excluded by PLIP PO4.12: 5 residues within 4Å: Chain C: D.224, T.225, C.226, G.227, T.228 Ligand excluded by PLIP PO4.13: 6 residues within 4Å: Chain C: S.308, V.309, S.310 Chain D: R.104 Chain E: S.47, R.49 Ligand excluded by PLIP PO4.17: 5 residues within 4Å: Chain D: D.224, T.225, C.226, G.227, T.228 Ligand excluded by PLIP PO4.18: 6 residues within 4Å: Chain B: S.47, R.49 Chain C: R.104 Chain D: S.308, V.309, S.310 Ligand excluded by PLIP PO4.22: 5 residues within 4Å: Chain E: D.224, T.225, C.226, G.227, T.228 Ligand excluded by PLIP PO4.23: 6 residues within 4Å: Chain A: S.47, R.49 Chain E: S.308, V.309, S.310 Chain F: R.104 Ligand excluded by PLIP PO4.27: 5 residues within 4Å: Chain F: D.224, T.225, C.226, G.227, T.228 Ligand excluded by PLIP PO4.28: 6 residues within 4Å: Chain D: S.47, R.49 Chain E: R.104 Chain F: S.308, V.309, S.310 Ligand excluded by PLIP PO4.32: 5 residues within 4Å: Chain G: D.224, T.225, C.226, G.227, T.228 Ligand excluded by PLIP PO4.33: 6 residues within 4Å: Chain G: S.308, V.309, S.310 Chain H: R.104 Chain I: S.47, R.49 Ligand excluded by PLIP PO4.37: 5 residues within 4Å: Chain H: D.224, T.225, C.226, G.227, T.228 Ligand excluded by PLIP PO4.38: 6 residues within 4Å: Chain G: R.104 Chain H: S.308, V.309, S.310 Chain L: S.47, R.49 Ligand excluded by PLIP PO4.42: 5 residues within 4Å: Chain I: D.224, T.225, C.226, G.227, T.228 Ligand excluded by PLIP PO4.43: 6 residues within 4Å: Chain I: S.308, V.309, S.310 Chain J: R.104 Chain K: S.47, R.49 Ligand excluded by PLIP PO4.47: 5 residues within 4Å: Chain J: D.224, T.225, C.226, G.227, T.228 Ligand excluded by PLIP PO4.48: 6 residues within 4Å: Chain H: S.47, R.49 Chain I: R.104 Chain J: S.308, V.309, S.310 Ligand excluded by PLIP PO4.52: 5 residues within 4Å: Chain K: D.224, T.225, C.226, G.227, T.228 Ligand excluded by PLIP PO4.53: 6 residues within 4Å: Chain G: S.47, R.49 Chain K: S.308, V.309, S.310 Chain L: R.104 Ligand excluded by PLIP PO4.57: 5 residues within 4Å: Chain L: D.224, T.225, C.226, G.227, T.228 Ligand excluded by PLIP PO4.58: 6 residues within 4Å: Chain J: S.47, R.49 Chain K: R.104 Chain L: S.308, V.309, S.310 Ligand excluded by PLIP

24 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: 1 residues within 4Å: Chain A: D.171 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.171 MG.9: 2 residues within 4Å: Chain B: 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: 1 residues within 4Å: Chain B: D.171 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.171 MG.14: 2 residues within 4Å: Chain C: 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: 1 residues within 4Å: Chain C: D.171 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.171 MG.19: 2 residues within 4Å: Chain D: 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: 1 residues within 4Å: Chain D: D.171 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.171 MG.24: 2 residues within 4Å: Chain E: 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: 1 residues within 4Å: Chain E: D.171 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.171 MG.29: 2 residues within 4Å: Chain F: 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: 1 residues within 4Å: Chain F: D.171 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.171 MG.34: 2 residues within 4Å: Chain G: 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: 1 residues within 4Å: Chain G: D.171 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.171 MG.39: 2 residues within 4Å: Chain H: 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: 1 residues within 4Å: Chain H: D.171 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.171 MG.44: 2 residues within 4Å: Chain I: 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: 1 residues within 4Å: Chain I: D.171 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:D.171 MG.49: 2 residues within 4Å: Chain J: 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: 1 residues within 4Å: Chain J: D.171 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.171 MG.54: 2 residues within 4Å: Chain K: 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: 1 residues within 4Å: Chain K: D.171 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.171 MG.59: 2 residues within 4Å: Chain L: 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: 1 residues within 4Å: Chain L: D.171 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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