SMTL ID : 8dbe.1

Human PRPS1 with ADP; Hexamer

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.130, D.171, D.220, D.221, M.222, D.224, T.225, C.226, G.227, T.228 Ligands: ADP.3, MG.5 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.220, A:D.224, A:T.225, A:T.225, A:C.226, 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: ADP.6, MG.10 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:H.130, B:D.220, B:D.224, B:T.225, B:C.226, B:T.228, B:T.228, B:T.228 Salt bridges: B:H.130 HSX.11: 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: ADP.13, MG.15 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:D.220, C:D.224, C:T.225, C:T.225, C:C.226, C:T.228, C:T.228 Salt bridges: C:H.130 HSX.16: 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: ADP.18, MG.20 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:H.130, D:D.220, D:D.224, D:T.225, D:C.226, D:T.228, D:T.228, D:T.228 Salt bridges: D:H.130 HSX.21: 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: ADP.23, MG.25 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:D.220, E:D.224, E:T.225, E:T.225, E:C.226, 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: ADP.26, MG.30 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:H.130, F:D.220, F:D.224, F:T.225, F:C.226, F:T.228, F:T.228, F:T.228 Salt bridges: F:H.130

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

ADP.2: 16 residues within 4Å: Chain A: Q.135, V.142, D.143, N.144, Y.146, S.308, V.309, S.310, F.313 Chain E: R.49, A.80 Chain F: K.100, D.101, K.102, S.103, R.104 19 PLIP interactions: 10 interactions with chain A, 3 interactions with chain E, 6 interactions with chain F Hydrogen bonds: A:Q.135, A:D.143, A:D.143, A:N.144, A:N.144, A:S.308, A:V.309, A:S.310, F:R.104 pi-Stacking: A:F.313, A:F.313 Water bridges: E:I.79, F:K.100, F:R.104, F:R.104 Salt bridges: E:R.49, E:R.49, F:K.100, F:R.104 ADP.3: 13 residues within 4Å: Chain A: R.96, Q.97, K.99, D.101, K.102, H.130, D.224 Chain B: F.35, N.37, E.39 Chain F: K.176 Ligands: HSX.1, MG.4 13 PLIP interactions: 8 interactions with chain A, 1 interactions with chain F, 4 interactions with chain B Hydrogen bonds: A:D.101, A:D.224, B:N.37, B:N.37 Water bridges: A:K.99, A:K.99, A:K.99 Salt bridges: A:K.99, A:K.99, A:H.130, F:K.176 pi-Stacking: B:F.35, B:F.35 ADP.6: 13 residues within 4Å: Chain A: F.35, N.37, E.39 Chain B: R.96, Q.97, K.99, D.101, K.102, H.130, D.224 Chain C: K.176 Ligands: HSX.7, MG.9 12 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C, 7 interactions with chain B Hydrogen bonds: A:N.37, A:N.37 pi-Stacking: A:F.35, A:F.35 Salt bridges: C:K.176, B:K.99, B:K.99, B:H.130 Water bridges: B:K.99, B:K.99, B:K.99, B:H.130 ADP.8: 16 residues within 4Å: Chain B: Q.135, V.142, D.143, N.144, Y.146, S.308, V.309, S.310, F.313 Chain C: K.100, D.101, K.102, S.103, R.104 Chain D: R.49, A.80 20 PLIP interactions: 4 interactions with chain D, 10 interactions with chain B, 6 interactions with chain C Hydrogen bonds: D:A.80, B:Q.135, B:D.143, B:N.144, B:N.144, B:S.308, B:V.309, B:S.310, C:R.104 Water bridges: D:I.79, B:Y.146, C:K.100, C:R.104, C:R.104 Salt bridges: D:R.49, D:R.49, C:K.100, C:R.104 pi-Stacking: B:F.313, B:F.313 ADP.12: 16 residues within 4Å: Chain A: R.49, A.80 Chain B: K.100, D.101, K.102, S.103, R.104 Chain C: Q.135, V.142, D.143, N.144, Y.146, S.308, V.309, S.310, F.313 19 PLIP interactions: 10 interactions with chain C, 6 interactions with chain B, 3 interactions with chain A Hydrogen bonds: C:Q.135, C:D.143, C:D.143, C:N.144, C:N.144, C:S.308, C:V.309, C:S.310, B:R.104 pi-Stacking: C:F.313, C:F.313 Water bridges: B:K.100, B:R.104, B:R.104, A:I.79 Salt bridges: B:K.100, B:R.104, A:R.49, A:R.49 ADP.13: 13 residues within 4Å: Chain B: K.176 Chain C: R.96, Q.97, K.99, D.101, K.102, H.130, D.224 Chain D: F.35, N.37, E.39 Ligands: HSX.11, MG.14 13 PLIP interactions: 8 interactions with chain C, 1 interactions with chain B, 4 interactions with chain D Hydrogen bonds: C:D.101, C:D.224, D:N.37, D:N.37 Water bridges: C:K.99, C:K.99, C:K.99 Salt bridges: C:K.99, C:K.99, C:H.130, B:K.176 pi-Stacking: D:F.35, D:F.35 ADP.17: 16 residues within 4Å: Chain D: Q.135, V.142, D.143, N.144, Y.146, S.308, V.309, S.310, F.313 Chain E: K.100, D.101, K.102, S.103, R.104 Chain F: R.49, A.80 20 PLIP interactions: 10 interactions with chain D, 6 interactions with chain E, 4 interactions with chain F Hydrogen bonds: D:Q.135, D:D.143, D:N.144, D:N.144, D:S.308, D:V.309, D:S.310, E:R.104, F:A.80 Water bridges: D:Y.146, E:K.100, E:R.104, E:R.104, F:I.79 pi-Stacking: D:F.313, D:F.313 Salt bridges: E:K.100, E:R.104, F:R.49, F:R.49 ADP.18: 13 residues within 4Å: Chain C: F.35, N.37, E.39 Chain D: R.96, Q.97, K.99, D.101, K.102, H.130, D.224 Chain E: K.176 Ligands: HSX.16, MG.19 12 PLIP interactions: 4 interactions with chain C, 1 interactions with chain E, 7 interactions with chain D Hydrogen bonds: C:N.37, C:N.37 pi-Stacking: C:F.35, C:F.35 Salt bridges: E:K.176, D:K.99, D:K.99, D:H.130 Water bridges: D:K.99, D:K.99, D:K.99, D:H.130 ADP.22: 16 residues within 4Å: Chain C: R.49, A.80 Chain D: K.100, D.101, K.102, S.103, R.104 Chain E: Q.135, V.142, D.143, N.144, Y.146, S.308, V.309, S.310, F.313 19 PLIP interactions: 6 interactions with chain D, 10 interactions with chain E, 3 interactions with chain C Hydrogen bonds: D:R.104, E:Q.135, E:D.143, E:D.143, E:N.144, E:N.144, E:S.308, E:V.309, E:S.310 Water bridges: D:K.100, D:R.104, D:R.104, C:I.79 Salt bridges: D:K.100, D:R.104, C:R.49, C:R.49 pi-Stacking: E:F.313, E:F.313 ADP.23: 13 residues within 4Å: Chain D: K.176 Chain E: R.96, Q.97, K.99, D.101, K.102, H.130, D.224 Chain F: F.35, N.37, E.39 Ligands: HSX.21, MG.24 13 PLIP interactions: 8 interactions with chain E, 4 interactions with chain F, 1 interactions with chain D Hydrogen bonds: E:D.101, E:D.224, F:N.37, F:N.37 Water bridges: E:K.99, E:K.99, E:K.99 Salt bridges: E:K.99, E:K.99, E:H.130, D:K.176 pi-Stacking: F:F.35, F:F.35 ADP.26: 13 residues within 4Å: Chain A: K.176 Chain E: F.35, N.37, E.39 Chain F: R.96, Q.97, K.99, D.101, K.102, H.130, D.224 Ligands: HSX.27, MG.29 12 PLIP interactions: 4 interactions with chain E, 7 interactions with chain F, 1 interactions with chain A Hydrogen bonds: E:N.37, E:N.37 pi-Stacking: E:F.35, E:F.35 Water bridges: F:K.99, F:K.99, F:K.99, F:H.130 Salt bridges: F:K.99, F:K.99, F:H.130, A:K.176 ADP.28: 16 residues within 4Å: Chain A: K.100, D.101, K.102, S.103, R.104 Chain B: R.49, A.80 Chain F: Q.135, V.142, D.143, N.144, Y.146, S.308, V.309, S.310, F.313 20 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A, 10 interactions with chain F Hydrogen bonds: B:A.80, A:R.104, F:Q.135, F:D.143, F:N.144, F:N.144, F:S.308, F:V.309, F:S.310 Water bridges: B:I.79, A:K.100, A:R.104, A:R.104, F:Y.146 Salt bridges: B:R.49, B:R.49, A:K.100, A:R.104 pi-Stacking: F:F.313, F:F.313

12 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: K.99, H.130 Ligands: ADP.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.130, H2O.1, H2O.1, H2O.1 MG.5: 2 residues within 4Å: Chain A: D.171 Ligands: HSX.1 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: ADP.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.130, H2O.1, H2O.1, H2O.1 MG.10: 2 residues within 4Å: Chain B: D.171 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: ADP.13 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:H.130, H2O.1, H2O.1, H2O.1 MG.15: 2 residues within 4Å: Chain C: D.171 Ligands: HSX.11 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: ADP.18 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:H.130, H2O.1, H2O.2, H2O.2 MG.20: 2 residues within 4Å: Chain D: D.171 Ligands: HSX.16 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: ADP.23 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:H.130, H2O.2, H2O.2, H2O.2 MG.25: 2 residues within 4Å: Chain E: D.171 Ligands: HSX.21 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: ADP.26 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:H.130, H2O.2, H2O.2, H2O.2 MG.30: 2 residues within 4Å: Chain F: D.171 Ligands: HSX.27 1 PLIP interactions: 1 interactions with chain F Metal complexes: F: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: 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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