SMTL ID : 8dbm.1

Human PRPS1 with Phosphate and PRPP; Filament Interface

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

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

PRP.1: 14 residues within 4Å: Chain A: H.130, D.171, G.173, D.220, D.221, M.222, A.223, D.224, T.225, C.226, G.227, T.228 Ligands: MG.3, MG.4 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:G.173, A:D.220, A:D.224, A:T.225, A:T.225, A:C.226, A:G.227, A:T.228, A:T.228, A:T.228 Water bridges: A:K.99, A:K.99 Salt bridges: A:H.130, A:H.130, A:H.130 PRP.5: 14 residues within 4Å: Chain B: H.130, D.171, G.173, D.220, D.221, M.222, A.223, D.224, T.225, C.226, G.227, T.228 Ligands: MG.7, MG.8 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.173, B:D.220, B:D.224, B:T.225, B:C.226, B:G.227, B:T.228, B:T.228 Water bridges: B:K.99, B:K.99 Salt bridges: B:H.130, B:H.130, B:H.130 PRP.9: 14 residues within 4Å: Chain C: H.130, D.171, G.173, D.220, D.221, M.222, A.223, D.224, T.225, C.226, G.227, T.228 Ligands: MG.11, MG.12 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:G.173, C:D.220, C:D.224, C:T.225, C:T.225, C:C.226, C:G.227, C:T.228, C:T.228, C:T.228 Water bridges: C:K.99, C:K.99 Salt bridges: C:H.130, C:H.130, C:H.130 PRP.13: 14 residues within 4Å: Chain D: H.130, D.171, G.173, D.220, D.221, M.222, A.223, D.224, T.225, C.226, G.227, T.228 Ligands: MG.15, MG.16 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:G.173, D:D.220, D:D.221, D:D.224, D:T.225, D:C.226, D:G.227, D:T.228, D:T.228 Water bridges: D:K.99, D:K.99 Salt bridges: D:H.130, D:H.130, D:H.130 PRP.17: 14 residues within 4Å: Chain E: H.130, D.171, G.173, D.220, D.221, M.222, A.223, D.224, T.225, C.226, G.227, T.228 Ligands: MG.19, MG.20 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:G.173, E:D.220, E:D.224, E:T.225, E:T.225, E:C.226, E:G.227, E:T.228, E:T.228, E:T.228 Water bridges: E:K.99, E:K.99 Salt bridges: E:H.130, E:H.130, E:H.130 PRP.21: 14 residues within 4Å: Chain F: H.130, D.171, G.173, D.220, D.221, M.222, A.223, D.224, T.225, C.226, G.227, T.228 Ligands: MG.23, MG.24 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:G.173, F:D.220, F:D.224, F:T.225, F:C.226, F:G.227, F:T.228, F:T.228 Water bridges: F:K.99, F:K.99 Salt bridges: F:H.130, F:H.130, F:H.130 PRP.25: 14 residues within 4Å: Chain G: H.130, D.171, G.173, D.220, D.221, M.222, A.223, D.224, T.225, C.226, G.227, T.228 Ligands: MG.27, MG.28 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:G.173, G:D.220, G:D.224, G:T.225, G:T.225, G:C.226, G:G.227, G:T.228, G:T.228, G:T.228 Water bridges: G:K.99, G:K.99 Salt bridges: G:H.130, G:H.130, G:H.130 PRP.29: 14 residues within 4Å: Chain H: H.130, D.171, G.173, D.220, D.221, M.222, A.223, D.224, T.225, C.226, G.227, T.228 Ligands: MG.31, MG.32 14 PLIP interactions: 14 interactions with chain H Hydrogen bonds: H:G.173, H:D.220, H:D.221, H:D.224, H:T.225, H:C.226, H:G.227, H:T.228, H:T.228 Water bridges: H:K.99, H:K.99 Salt bridges: H:H.130, H:H.130, H:H.130 PRP.33: 14 residues within 4Å: Chain I: H.130, D.171, G.173, D.220, D.221, M.222, A.223, D.224, T.225, C.226, G.227, T.228 Ligands: MG.35, MG.36 15 PLIP interactions: 15 interactions with chain I Hydrogen bonds: I:G.173, I:D.220, I:D.224, I:T.225, I:T.225, I:C.226, I:G.227, I:T.228, I:T.228, I:T.228 Water bridges: I:K.99, I:K.99 Salt bridges: I:H.130, I:H.130, I:H.130 PRP.37: 14 residues within 4Å: Chain J: H.130, D.171, G.173, D.220, D.221, M.222, A.223, D.224, T.225, C.226, G.227, T.228 Ligands: MG.39, MG.40 13 PLIP interactions: 13 interactions with chain J Hydrogen bonds: J:G.173, J:D.220, J:D.224, J:T.225, J:C.226, J:G.227, J:T.228, J:T.228 Water bridges: J:K.99, J:K.99 Salt bridges: J:H.130, J:H.130, J:H.130 PRP.41: 14 residues within 4Å: Chain K: H.130, D.171, G.173, D.220, D.221, M.222, A.223, D.224, T.225, C.226, G.227, T.228 Ligands: MG.43, MG.44 15 PLIP interactions: 15 interactions with chain K Hydrogen bonds: K:G.173, K:D.220, K:D.224, K:T.225, K:T.225, K:C.226, K:G.227, K:T.228, K:T.228, K:T.228 Water bridges: K:K.99, K:K.99 Salt bridges: K:H.130, K:H.130, K:H.130 PRP.45: 14 residues within 4Å: Chain L: H.130, D.171, G.173, D.220, D.221, M.222, A.223, D.224, T.225, C.226, G.227, T.228 Ligands: MG.47, MG.48 14 PLIP interactions: 14 interactions with chain L Hydrogen bonds: L:G.173, L:D.220, L:D.221, L:D.224, L:T.225, L:C.226, L:G.227, L:T.228, L:T.228 Water bridges: L:K.99, L:K.99 Salt bridges: L:H.130, L:H.130, L:H.130

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

PO4.2: 7 residues within 4Å: Chain A: E.307, S.308, V.309, S.310 Chain E: S.47, R.49 Chain F: R.104 6 PLIP interactions: 4 interactions with chain A, 1 interactions with chain E, 1 interactions with chain F Hydrogen bonds: A:S.308, A:S.308, A:V.309, A:S.310 Salt bridges: E:R.49, F:R.104 PO4.6: 7 residues within 4Å: Chain B: E.307, S.308, V.309, S.310 Chain C: R.104 Chain D: S.47, R.49 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: B:V.309, B:S.310, B:S.310 Salt bridges: C:R.104, D:R.49 PO4.10: 7 residues within 4Å: Chain A: S.47, R.49 Chain B: R.104 Chain C: E.307, S.308, V.309, S.310 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: C:S.308, C:V.309, C:S.310 Salt bridges: B:R.104, A:R.49 PO4.14: 7 residues within 4Å: Chain D: E.307, S.308, V.309, S.310 Chain E: R.104 Chain F: S.47, R.49 5 PLIP interactions: 1 interactions with chain E, 3 interactions with chain D, 1 interactions with chain F Salt bridges: E:R.104, F:R.49 Hydrogen bonds: D:V.309, D:S.310, D:S.310 PO4.18: 7 residues within 4Å: Chain C: S.47, R.49 Chain D: R.104 Chain E: E.307, S.308, V.309, S.310 6 PLIP interactions: 4 interactions with chain E, 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: E:S.308, E:S.308, E:V.309, E:S.310 Salt bridges: C:R.49, D:R.104 PO4.22: 7 residues within 4Å: Chain A: R.104 Chain B: S.47, R.49 Chain F: E.307, S.308, V.309, S.310 5 PLIP interactions: 1 interactions with chain B, 3 interactions with chain F, 1 interactions with chain A Salt bridges: B:R.49, A:R.104 Hydrogen bonds: F:V.309, F:S.310, F:S.310 PO4.26: 7 residues within 4Å: Chain G: E.307, S.308, V.309, S.310 Chain K: S.47, R.49 Chain L: R.104 6 PLIP interactions: 1 interactions with chain L, 4 interactions with chain G, 1 interactions with chain K Salt bridges: L:R.104, K:R.49 Hydrogen bonds: G:E.307, G:S.308, G:V.309, G:S.310 PO4.30: 7 residues within 4Å: Chain H: E.307, S.308, V.309, S.310 Chain I: R.104 Chain J: S.47, R.49 5 PLIP interactions: 1 interactions with chain J, 3 interactions with chain H, 1 interactions with chain I Salt bridges: J:R.49, I:R.104 Hydrogen bonds: H:V.309, H:S.310, H:S.310 PO4.34: 7 residues within 4Å: Chain G: S.47, R.49 Chain H: R.104 Chain I: E.307, S.308, V.309, S.310 5 PLIP interactions: 1 interactions with chain G, 3 interactions with chain I, 1 interactions with chain H Salt bridges: G:R.49, H:R.104 Hydrogen bonds: I:E.307, I:V.309, I:S.310 PO4.38: 7 residues within 4Å: Chain J: E.307, S.308, V.309, S.310 Chain K: R.104 Chain L: S.47, R.49 5 PLIP interactions: 1 interactions with chain L, 3 interactions with chain J, 1 interactions with chain K Salt bridges: L:R.49, K:R.104 Hydrogen bonds: J:V.309, J:S.310, J:S.310 PO4.42: 7 residues within 4Å: Chain I: S.47, R.49 Chain J: R.104 Chain K: E.307, S.308, V.309, S.310 6 PLIP interactions: 4 interactions with chain K, 1 interactions with chain J, 1 interactions with chain I Hydrogen bonds: K:S.308, K:S.308, K:V.309, K:S.310 Salt bridges: J:R.104, I:R.49 PO4.46: 7 residues within 4Å: Chain G: R.104 Chain H: S.47, R.49 Chain L: E.307, S.308, V.309, S.310 5 PLIP interactions: 1 interactions with chain G, 3 interactions with chain L, 1 interactions with chain H Salt bridges: G:R.104, H:R.49 Hydrogen bonds: L:V.309, L:S.310, L:S.310

24 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: H.130 Ligands: PRP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.130, H2O.1, H2O.1 MG.4: 2 residues within 4Å: Chain A: D.171 Ligands: PRP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.171 MG.7: 2 residues within 4Å: Chain B: H.130 Ligands: PRP.5 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.130, H2O.1, H2O.1 MG.8: 2 residues within 4Å: Chain B: D.171 Ligands: PRP.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.171 MG.11: 2 residues within 4Å: Chain C: H.130 Ligands: PRP.9 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.130, H2O.1, H2O.1 MG.12: 2 residues within 4Å: Chain C: D.171 Ligands: PRP.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.171 MG.15: 2 residues within 4Å: Chain D: H.130 Ligands: PRP.13 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.130, H2O.1, H2O.1 MG.16: 2 residues within 4Å: Chain D: D.171 Ligands: PRP.13 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.171 MG.19: 2 residues within 4Å: Chain E: H.130 Ligands: PRP.17 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.130, H2O.1, H2O.1 MG.20: 2 residues within 4Å: Chain E: D.171 Ligands: PRP.17 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.171 MG.23: 2 residues within 4Å: Chain F: H.130 Ligands: PRP.21 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.130, H2O.1, H2O.1 MG.24: 2 residues within 4Å: Chain F: D.171 Ligands: PRP.21 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.171 MG.27: 2 residues within 4Å: Chain G: H.130 Ligands: PRP.25 3 PLIP interactions: 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:H.130, H2O.1, H2O.1 MG.28: 2 residues within 4Å: Chain G: D.171 Ligands: PRP.25 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.171 MG.31: 2 residues within 4Å: Chain H: H.130 Ligands: PRP.29 3 PLIP interactions: 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:H.130, H2O.1, H2O.1 MG.32: 2 residues within 4Å: Chain H: D.171 Ligands: PRP.29 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.171 MG.35: 2 residues within 4Å: Chain I: H.130 Ligands: PRP.33 3 PLIP interactions: 1 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:H.130, H2O.1, H2O.1 MG.36: 2 residues within 4Å: Chain I: D.171 Ligands: PRP.33 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:D.171 MG.39: 2 residues within 4Å: Chain J: H.130 Ligands: PRP.37 3 PLIP interactions: 1 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:H.130, H2O.1, H2O.1 MG.40: 2 residues within 4Å: Chain J: D.171 Ligands: PRP.37 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.171 MG.43: 2 residues within 4Å: Chain K: H.130 Ligands: PRP.41 3 PLIP interactions: 1 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:H.130, H2O.1, H2O.1 MG.44: 2 residues within 4Å: Chain K: D.171 Ligands: PRP.41 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.171 MG.47: 2 residues within 4Å: Chain L: H.130 Ligands: PRP.45 3 PLIP interactions: 1 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:H.130, H2O.1, H2O.1 MG.48: 2 residues within 4Å: Chain L: D.171 Ligands: PRP.45 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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