SMTL ID : 8dbn.1

Human PRPS1-E307A engineered mutation with Phosphate, ATP, and R5P; Hexamer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

ATP.1: 13 residues within 4Å: Chain A: R.96, Q.97, K.99, K.102, H.130, G.173, D.224 Chain B: F.35, N.37, E.39 Chain F: K.176 Ligands: HSX.2, MG.3 13 PLIP interactions: 7 interactions with chain A, 2 interactions with chain F, 4 interactions with chain B Hydrogen bonds: A:Q.97, A:K.102, A:K.102, A:D.224, B:E.39, B:E.39 Salt bridges: A:K.99, A:K.99, A:H.130, F:K.176, F:K.176 pi-Stacking: B:F.35, B:F.35 ATP.5: 13 residues within 4Å: Chain A: F.35, N.37, E.39 Chain B: R.96, Q.97, K.99, K.102, H.130, G.173, D.224 Chain C: K.176 Ligands: HSX.6, MG.7 11 PLIP interactions: 2 interactions with chain C, 6 interactions with chain B, 3 interactions with chain A Salt bridges: C:K.176, C:K.176, B:K.99, B:K.99, B:H.130 Hydrogen bonds: B:Q.97, B:K.102, B:K.102, A:E.39 pi-Stacking: A:F.35, A:F.35 ATP.9: 13 residues within 4Å: Chain B: K.176 Chain C: R.96, Q.97, K.99, K.102, H.130, G.173, D.224 Chain D: F.35, N.37, E.39 Ligands: HSX.10, MG.11 13 PLIP interactions: 7 interactions with chain C, 4 interactions with chain D, 2 interactions with chain B Hydrogen bonds: C:Q.97, C:K.102, C:K.102, C:D.224, D:E.39, D:E.39 Salt bridges: C:K.99, C:K.99, C:H.130, B:K.176, B:K.176 pi-Stacking: D:F.35, D:F.35 ATP.13: 13 residues within 4Å: Chain C: F.35, N.37, E.39 Chain D: R.96, Q.97, K.99, K.102, H.130, G.173, D.224 Chain E: K.176 Ligands: HSX.14, MG.15 11 PLIP interactions: 6 interactions with chain D, 3 interactions with chain C, 2 interactions with chain E Hydrogen bonds: D:Q.97, D:K.102, D:K.102, C:E.39 Salt bridges: D:K.99, D:K.99, D:H.130, E:K.176, E:K.176 pi-Stacking: C:F.35, C:F.35 ATP.17: 13 residues within 4Å: Chain D: K.176 Chain E: R.96, Q.97, K.99, K.102, H.130, G.173, D.224 Chain F: F.35, N.37, E.39 Ligands: HSX.18, MG.19 13 PLIP interactions: 2 interactions with chain D, 7 interactions with chain E, 4 interactions with chain F Salt bridges: D:K.176, D:K.176, E:K.99, E:K.99, E:H.130 Hydrogen bonds: E:Q.97, E:K.102, E:K.102, E:D.224, F:E.39, F:E.39 pi-Stacking: F:F.35, F:F.35 ATP.21: 13 residues within 4Å: Chain A: K.176 Chain E: F.35, N.37, E.39 Chain F: R.96, Q.97, K.99, K.102, H.130, G.173, D.224 Ligands: HSX.22, MG.23 11 PLIP interactions: 6 interactions with chain F, 2 interactions with chain A, 3 interactions with chain E Hydrogen bonds: F:Q.97, F:K.102, F:K.102, E:E.39 Salt bridges: F:K.99, F:K.99, F:H.130, A:K.176, A:K.176 pi-Stacking: E:F.35, E:F.35

6 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.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:H.130, A:D.224, A:T.225, A:C.226, A:G.227, A:T.228, A:T.228, A:T.228 HSX.6: 13 residues within 4Å: Chain B: H.130, D.171, D.220, D.221, M.222, A.223, D.224, T.225, C.226, G.227, T.228 Ligands: ATP.5, MG.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:H.130, B:D.224, B:T.225, B:C.226, B:G.227, B:T.228, B:T.228, B:T.228 HSX.10: 13 residues within 4Å: Chain C: H.130, D.171, D.220, D.221, M.222, A.223, D.224, T.225, C.226, G.227, T.228 Ligands: ATP.9, MG.12 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:H.130, C:D.224, C:T.225, C:C.226, C:G.227, C:T.228, C:T.228, C:T.228 HSX.14: 13 residues within 4Å: Chain D: H.130, D.171, D.220, D.221, M.222, A.223, D.224, T.225, C.226, G.227, T.228 Ligands: ATP.13, MG.16 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:H.130, D:D.221, D:D.224, D:T.225, D:C.226, D:G.227, D:T.228, D:T.228, D:T.228 HSX.18: 13 residues within 4Å: Chain E: H.130, D.171, D.220, D.221, M.222, A.223, D.224, T.225, C.226, G.227, T.228 Ligands: ATP.17, MG.20 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:H.130, E:D.224, E:T.225, E:C.226, E:G.227, E:T.228, E:T.228, E:T.228 HSX.22: 13 residues within 4Å: Chain F: H.130, D.171, D.220, D.221, M.222, A.223, D.224, T.225, C.226, G.227, T.228 Ligands: ATP.21, MG.24 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:H.130, F:D.224, F:T.225, F:C.226, F:G.227, F:T.228, F:T.228, F:T.228

12 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: K.99, H.130 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.130 MG.4: 4 residues within 4Å: Chain A: D.171, D.220, D.221 Ligands: HSX.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.171, A:D.171 MG.7: 3 residues within 4Å: Chain B: K.99, H.130 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.130 MG.8: 4 residues within 4Å: Chain B: D.171, D.220, D.221 Ligands: HSX.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.171, B:D.171 MG.11: 3 residues within 4Å: Chain C: K.99, H.130 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.130 MG.12: 4 residues within 4Å: Chain C: D.171, D.220, D.221 Ligands: HSX.10 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.171, C:D.171 MG.15: 3 residues within 4Å: Chain D: K.99, H.130 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.130 MG.16: 4 residues within 4Å: Chain D: D.171, D.220, D.221 Ligands: HSX.14 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.171, D:D.171 MG.19: 3 residues within 4Å: Chain E: K.99, H.130 Ligands: ATP.17 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:H.130 MG.20: 4 residues within 4Å: Chain E: D.171, D.220, D.221 Ligands: HSX.18 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.171, E:D.171 MG.23: 3 residues within 4Å: Chain F: K.99, H.130 Ligands: ATP.21 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:H.130 MG.24: 4 residues within 4Å: Chain F: D.171, D.220, D.221 Ligands: HSX.22 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.171, 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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