SMTL ID : 8yi9.1

human PRPS2 isoform2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x RP5: 5-O-phosphono-beta-D-ribofuranose(Non-covalent)

RP5.1: 14 residues within 4Å: Chain A: R.96, H.133, D.174, D.223, D.224, M.225, A.226, D.227, T.228, C.229, G.230, T.231 Ligands: MG.2, ADP.21 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:D.224, A:D.227, A:T.228, A:C.229, A:G.230, A:T.231, A:T.231, A:T.231 Salt bridges: A:R.96, A:H.133 RP5.5: 14 residues within 4Å: Chain B: R.96, H.133, D.174, D.223, D.224, M.225, A.226, D.227, T.228, C.229, G.230, T.231 Ligands: MG.6, ADP.17 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.223, B:D.227, B:T.228, B:C.229, B:G.230, B:T.231, B:T.231, B:T.231 Salt bridges: B:H.133 RP5.9: 14 residues within 4Å: Chain C: R.96, H.133, D.174, D.223, D.224, M.225, A.226, D.227, T.228, C.229, G.230, T.231 Ligands: MG.10, ADP.13 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:D.224, C:D.227, C:T.228, C:C.229, C:G.230, C:T.231, C:T.231 Salt bridges: C:H.133 RP5.14: 14 residues within 4Å: Chain D: R.96, H.133, D.174, D.223, D.224, M.225, A.226, D.227, T.228, C.229, G.230, T.231 Ligands: ADP.12, MG.15 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:D.224, D:D.227, D:T.228, D:C.229, D:G.230, D:T.231, D:T.231 Salt bridges: D:R.96, D:H.133 RP5.18: 14 residues within 4Å: Chain E: R.96, H.133, D.174, D.223, D.224, M.225, A.226, D.227, T.228, C.229, G.230, T.231 Ligands: ADP.8, MG.19 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:D.223, E:D.227, E:T.228, E:C.229, E:G.230, E:T.231, E:T.231 Salt bridges: E:H.133 RP5.22: 14 residues within 4Å: Chain F: R.96, H.133, D.174, D.223, D.224, M.225, A.226, D.227, T.228, C.229, G.230, T.231 Ligands: ADP.4, MG.23 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:D.224, F:D.227, F:T.228, F:C.229, F:G.230, F:T.231 Salt bridges: F:H.133

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.174 Ligands: RP5.1, ADP.21 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.174 MG.3: 2 residues within 4Å: Chain A: H.133 Ligands: ADP.21 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.133 MG.6: 3 residues within 4Å: Chain B: D.174 Ligands: RP5.5, ADP.17 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.174 MG.7: 3 residues within 4Å: Chain B: K.99, H.133 Ligands: ADP.17 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.133 MG.10: 2 residues within 4Å: Chain C: D.174 Ligands: RP5.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.174 MG.11: 3 residues within 4Å: Chain C: K.99, H.133 Ligands: ADP.13 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.133 MG.15: 3 residues within 4Å: Chain D: D.174 Ligands: ADP.12, RP5.14 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.174 MG.16: 2 residues within 4Å: Chain D: H.133 Ligands: ADP.12 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.133 MG.19: 3 residues within 4Å: Chain E: D.174 Ligands: ADP.8, RP5.18 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.174 MG.20: 3 residues within 4Å: Chain E: K.99, H.133 Ligands: ADP.8 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:H.133 MG.23: 2 residues within 4Å: Chain F: D.174 Ligands: RP5.22 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.174 MG.24: 3 residues within 4Å: Chain F: K.99, H.133 Ligands: ADP.4 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:H.133

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

ADP.4: 12 residues within 4Å: Chain A: F.35, N.37, E.39 Chain C: K.179 Chain F: R.96, Q.97, K.99, D.101, H.133, D.227 Ligands: RP5.22, MG.24 9 PLIP interactions: 1 interactions with chain C, 3 interactions with chain F, 5 interactions with chain A Salt bridges: C:K.179, F:K.99, F:K.99 Hydrogen bonds: F:Q.97, A:N.37, A:N.37, A:E.39 pi-Stacking: A:F.35, A:F.35 ADP.8: 13 residues within 4Å: Chain A: K.179 Chain B: F.35, N.37, E.39 Chain E: R.96, Q.97, K.99, D.101, H.133, D.227 Ligands: RP5.18, MG.19, MG.20 9 PLIP interactions: 5 interactions with chain B, 3 interactions with chain E, 1 interactions with chain A Hydrogen bonds: B:N.37, B:N.37, B:E.39, E:Q.97 pi-Stacking: B:F.35, B:F.35 Salt bridges: E:K.99, E:K.99, A:K.179 ADP.12: 13 residues within 4Å: Chain B: K.179 Chain C: F.35, N.37, E.39 Chain D: R.96, Q.97, K.99, D.101, H.133, D.227 Ligands: RP5.14, MG.15, MG.16 9 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B, 5 interactions with chain C Hydrogen bonds: D:Q.97, C:N.37, C:N.37, C:E.39 Salt bridges: D:K.99, D:K.99, B:K.179 pi-Stacking: C:F.35, C:F.35 ADP.13: 12 residues within 4Å: Chain C: R.96, Q.97, K.99, D.101, H.133, D.227 Chain D: F.35, N.37, E.39 Chain F: K.179 Ligands: RP5.9, MG.11 9 PLIP interactions: 1 interactions with chain F, 4 interactions with chain D, 4 interactions with chain C Salt bridges: F:K.179, C:K.99, C:K.99 Hydrogen bonds: D:N.37, D:N.37, C:Q.97, C:E.105 pi-Stacking: D:F.35, D:F.35 ADP.17: 13 residues within 4Å: Chain B: R.96, Q.97, K.99, D.101, H.133, D.227 Chain D: K.179 Chain E: F.35, N.37, E.39 Ligands: RP5.5, MG.6, MG.7 9 PLIP interactions: 4 interactions with chain B, 4 interactions with chain E, 1 interactions with chain D Hydrogen bonds: B:Q.97, B:H.133, E:N.37, E:N.37 Salt bridges: B:K.99, B:K.99, D:K.179 pi-Stacking: E:F.35, E:F.35 ADP.21: 13 residues within 4Å: Chain A: R.96, Q.97, K.99, D.101, H.133, D.227 Chain E: K.179 Chain F: F.35, N.37, E.39 Ligands: RP5.1, MG.2, MG.3 9 PLIP interactions: 4 interactions with chain F, 4 interactions with chain A, 1 interactions with chain E Hydrogen bonds: F:N.37, F:N.37, A:Q.97, A:H.133 pi-Stacking: F:F.35, F:F.35 Salt bridges: A:K.99, A:K.99, E:K.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, J.L. et al., Structure of human PRPS2 long isoform at 3.4 Angstroms resolution. To Be Published

Release Date

2025-03-05

Peptides

Isoform 2 of Ribose-phosphate pyrophosphokinase 2: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Isoform 2 of Ribose-phosphate pyrophosphokinase 2