SMTL ID : 7yk1.1

Structural basis of human PRPS2 filaments

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

PO4.1: 6 residues within 4Å: Chain A: R.96, D.224, T.225, C.226, G.227, T.228 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.96, A:D.224, A:T.225, A:C.226, A:G.227, A:T.228 PO4.5: 7 residues within 4Å: Chain B: R.96, A.223, D.224, T.225, C.226, G.227, T.228 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.96, B:D.224, B:T.225, B:C.226, B:G.227, B:T.228, B:T.228, B:T.228, B:T.228 PO4.11: 5 residues within 4Å: Chain C: D.224, T.225, C.226, G.227, T.228 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:R.96, C:D.224, C:T.225, C:C.226, C:G.227, C:T.228, C:T.228, C:T.228 PO4.14: 7 residues within 4Å: Chain D: R.96, A.223, D.224, T.225, C.226, G.227, T.228 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:R.96, D:D.224, D:T.225, D:C.226, D:G.227, D:T.228, D:T.228, D:T.228, D:T.228 PO4.19: 5 residues within 4Å: Chain E: D.224, T.225, C.226, G.227, T.228 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:R.96, E:D.224, E:T.225, E:T.225, E:C.226, E:G.227, E:T.228 PO4.23: 6 residues within 4Å: Chain F: A.223, D.224, T.225, C.226, G.227, T.228 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:R.96, F:D.224, F:T.225, F:C.226, F:G.227, F:T.228, F:T.228

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.98, K.99, H.130 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.130 MG.6: 4 residues within 4Å: Chain B: D.98, K.99, H.130 Ligands: ADP.18 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.130 MG.12: 3 residues within 4Å: Chain C: K.99, H.130 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.130 MG.15: 4 residues within 4Å: Chain D: D.98, K.99, H.130 Ligands: ADP.21 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.130 MG.20: 3 residues within 4Å: Chain E: K.99, H.130 Ligands: ADP.8 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:H.130 MG.24: 4 residues within 4Å: Chain F: D.98, K.99, H.130 Ligands: ADP.16 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:H.130

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

ADP.3: 10 residues within 4Å: Chain A: F.35, N.37, E.39 Chain C: R.96, Q.97, K.99, H.130, D.224 Chain F: K.176 Ligands: MG.12 10 PLIP interactions: 5 interactions with chain C, 4 interactions with chain A, 1 interactions with chain F Hydrogen bonds: C:Q.97, A:N.37, A:E.39 Salt bridges: C:K.99, C:K.99, C:H.130, F:K.176 pi-Cation interactions: C:R.96 pi-Stacking: A:F.35, A:F.35 ADP.4: 15 residues within 4Å: Chain A: S.47, R.49 Chain C: K.100, D.101, K.102, S.103, R.104 Chain F: Q.135, D.143, N.144, E.307, S.308, V.309, S.310, F.313 13 PLIP interactions: 2 interactions with chain C, 7 interactions with chain F, 4 interactions with chain A Salt bridges: C:K.100, C:R.104, A:R.49, A:R.49 Hydrogen bonds: F:D.143, F:N.144, F:N.144, F:V.309, F:S.310, A:S.47, A:S.47 pi-Stacking: F:F.313, F:F.313 ADP.7: 15 residues within 4Å: Chain B: S.47, R.49 Chain D: Q.135, D.143, N.144, E.307, S.308, V.309, S.310, F.313 Chain E: K.100, D.101, K.102, S.103, R.104 13 PLIP interactions: 2 interactions with chain E, 7 interactions with chain D, 4 interactions with chain B Salt bridges: E:K.100, E:R.104, B:R.49, B:R.49 Hydrogen bonds: D:D.143, D:N.144, D:N.144, D:V.309, D:S.310, B:S.47, B:S.47 pi-Stacking: D:F.313, D:F.313 ADP.8: 10 residues within 4Å: Chain B: F.35, N.37, E.39 Chain D: K.176 Chain E: R.96, Q.97, K.99, H.130, D.224 Ligands: MG.20 12 PLIP interactions: 6 interactions with chain E, 5 interactions with chain B, 1 interactions with chain D Hydrogen bonds: E:Q.97, E:D.224, B:N.37, B:E.39, B:E.39 Salt bridges: E:K.99, E:K.99, E:H.130, D:K.176 pi-Cation interactions: E:R.96 pi-Stacking: B:F.35, B:F.35 ADP.9: 10 residues within 4Å: Chain A: R.96, Q.97, K.99, H.130, D.224 Chain B: K.176 Chain C: F.35, N.37, E.39 Ligands: MG.2 11 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C, 6 interactions with chain A Salt bridges: B:K.176, A:K.99, A:K.99, A:H.130 Hydrogen bonds: C:N.37, C:N.37, A:Q.97, A:D.224 pi-Stacking: C:F.35, C:F.35 pi-Cation interactions: A:R.96 ADP.10: 15 residues within 4Å: Chain A: K.100, D.101, K.102, S.103, R.104 Chain B: Q.135, D.143, N.144, E.307, S.308, V.309, S.310, F.313 Chain C: S.47, R.49 10 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A, 4 interactions with chain C Hydrogen bonds: B:N.144, B:V.309, C:S.47, C:S.47 pi-Stacking: B:F.313, B:F.313 Salt bridges: A:K.100, A:R.104, C:R.49, C:R.49 ADP.13: 16 residues within 4Å: Chain C: Q.135, V.142, D.143, N.144, E.307, S.308, V.309, S.310, F.313 Chain D: S.47, R.49 Chain F: K.100, D.101, K.102, S.103, R.104 12 PLIP interactions: 6 interactions with chain C, 4 interactions with chain D, 2 interactions with chain F Hydrogen bonds: C:D.143, C:N.144, C:V.309, C:S.310, D:S.47, D:S.47 pi-Stacking: C:F.313, C:F.313 Salt bridges: D:R.49, D:R.49, F:K.100, F:R.104 ADP.16: 10 residues within 4Å: Chain C: K.176 Chain D: F.35, N.37, E.39 Chain F: R.96, Q.97, K.99, H.130, D.224 Ligands: MG.24 11 PLIP interactions: 1 interactions with chain C, 5 interactions with chain F, 5 interactions with chain D Salt bridges: C:K.176, F:K.99, F:K.99, F:H.130 Hydrogen bonds: F:D.224, D:N.37, D:N.37, D:E.39 pi-Cation interactions: F:R.96 pi-Stacking: D:F.35, D:F.35 ADP.17: 15 residues within 4Å: Chain A: Q.135, D.143, N.144, E.307, S.308, V.309, S.310, F.313 Chain B: K.100, D.101, K.102, S.103, R.104 Chain E: S.47, R.49 12 PLIP interactions: 2 interactions with chain B, 4 interactions with chain E, 6 interactions with chain A Salt bridges: B:K.100, B:R.104, E:R.49, E:R.49 Hydrogen bonds: E:S.47, E:S.47, A:D.143, A:N.144, A:N.144, A:V.309 pi-Stacking: A:F.313, A:F.313 ADP.18: 10 residues within 4Å: Chain A: K.176 Chain B: R.96, Q.97, K.99, H.130, D.224 Chain E: F.35, N.37, E.39 Ligands: MG.6 10 PLIP interactions: 5 interactions with chain B, 4 interactions with chain E, 1 interactions with chain A Hydrogen bonds: B:Q.97, E:N.37, E:N.37 Salt bridges: B:K.99, B:K.99, B:H.130, A:K.176 pi-Cation interactions: B:R.96 pi-Stacking: E:F.35, E:F.35 ADP.21: 10 residues within 4Å: Chain D: R.96, Q.97, K.99, H.130, D.224 Chain E: K.176 Chain F: F.35, N.37, E.39 Ligands: MG.15 9 PLIP interactions: 4 interactions with chain F, 4 interactions with chain D, 1 interactions with chain E Hydrogen bonds: F:N.37, F:N.37 pi-Stacking: F:F.35, F:F.35 Salt bridges: D:K.99, D:K.99, D:H.130, E:K.176 pi-Cation interactions: D:R.96 ADP.22: 16 residues within 4Å: Chain D: K.100, D.101, K.102, S.103, R.104 Chain E: Q.135, V.142, D.143, N.144, E.307, S.308, V.309, S.310, F.313 Chain F: S.47, R.49 12 PLIP interactions: 6 interactions with chain E, 4 interactions with chain F, 2 interactions with chain D Hydrogen bonds: E:D.143, E:N.144, E:V.309, E:S.310, F:S.47, F:S.47 pi-Stacking: E:F.313, E:F.313 Salt bridges: F:R.49, F:R.49, D:K.100, D:R.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lu, G.M. et al., Structural basis of human PRPS2 filaments. Cell Biosci (2023)

Release Date

2023-08-02

Peptides

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

Ribose-phosphate pyrophosphokinase 2