SMTL ID : 8ypz.1

Crystal strcture of human phosphoribosyl pyrophosphate synthetase 1 (PRPS1) in complex with GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-hexamer

Ligands

6 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER

APC.1: 9 residues within 4Å: Chain A: R.96, Q.97, K.99, D.101, H.130, D.224 Chain F: F.35, N.37, E.39 9 PLIP interactions: 5 interactions with chain F, 4 interactions with chain A Hydrogen bonds: F:N.37, A:K.99, A:D.224 Water bridges: F:S.36, F:S.36 pi-Stacking: F:F.35, F:F.35 Salt bridges: A:K.99 pi-Cation interactions: A:R.96 APC.5: 9 residues within 4Å: Chain A: F.35, N.37, E.39 Chain E: K.176 Chain F: R.96, Q.97, K.99, D.101, H.130 9 PLIP interactions: 5 interactions with chain F, 3 interactions with chain A, 1 interactions with chain E Hydrogen bonds: F:Q.97, F:K.99, F:D.101, A:N.37, E:K.176 Salt bridges: F:K.99 pi-Cation interactions: F:R.96 pi-Stacking: A:F.35, A:F.35 APC.7: 9 residues within 4Å: Chain A: K.176 Chain B: R.96, Q.97, K.99, D.101, H.130 Chain C: F.35, N.37, E.39 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:N.37, B:Q.97, B:K.99 pi-Stacking: C:F.35, C:F.35 Salt bridges: B:K.99 pi-Cation interactions: B:R.96 APC.10: 10 residues within 4Å: Chain B: F.35, N.37, E.39 Chain C: R.96, Q.97, K.99, D.101, H.130, D.224 Chain D: K.176 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:R.96, C:K.99, C:K.99, C:D.224, B:N.37, B:E.39 Salt bridges: C:K.99 pi-Cation interactions: C:R.96 pi-Stacking: B:F.35, B:F.35 APC.15: 10 residues within 4Å: Chain C: K.176 Chain D: R.96, Q.97, K.99, D.101, H.130, D.224 Chain E: F.35, N.37, E.39 11 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C, 4 interactions with chain E Hydrogen bonds: D:Q.97, D:K.99, D:D.101, C:K.176, E:N.37, E:N.37 Salt bridges: D:K.99, D:K.102 pi-Cation interactions: D:R.96 pi-Stacking: E:F.35, E:F.35 APC.18: 8 residues within 4Å: Chain D: F.35, N.37, E.39 Chain E: R.96, Q.97, K.99, D.101, H.130 7 PLIP interactions: 3 interactions with chain E, 4 interactions with chain D Hydrogen bonds: E:K.99, D:N.37, D:E.39 Salt bridges: E:K.99 pi-Cation interactions: E:R.96 pi-Stacking: D:F.35, D:F.35

5 x HSX: 5-O-phosphono-alpha-D-ribofuranose

HSX.2: 8 residues within 4Å: Chain A: D.220, M.222, D.224, T.225, C.226, G.227, T.228, I.229 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.220, A:D.220, A:D.224, A:T.225, A:T.225, A:C.226, A:T.228, A:T.228, A:T.228, A:I.229 Salt bridges: A:K.194 HSX.8: 7 residues within 4Å: Chain B: D.220, M.222, T.225, C.226, G.227, T.228, I.229 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:D.220, B:T.225, B:T.225, B:T.225, B:C.226, B:G.227, B:T.228, B:T.228, B:I.229 Salt bridges: B:K.194 HSX.11: 6 residues within 4Å: Chain C: K.194, D.224, T.225, C.226, G.227, T.228 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:T.225, C:T.225, C:C.226, C:G.227, C:T.228, C:T.228 Salt bridges: C:K.194 HSX.19: 7 residues within 4Å: Chain E: A.223, D.224, T.225, C.226, G.227, T.228, I.229 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:A.223, E:D.224, E:T.225, E:T.225, E:C.226, E:G.227, E:T.228, E:T.228, E:I.229 HSX.22: 5 residues within 4Å: Chain F: D.224, T.225, C.226, G.227, T.228 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:D.224, F:T.225, F:G.227, F:T.228, F:T.228, F:T.228, F:T.228

6 x GDP: GUANOSINE-5'-DIPHOSPHATE

GDP.3: 16 residues within 4Å: Chain A: K.100, D.101, K.102, S.103, R.104 Chain B: D.143, N.144, Y.146, S.308, V.309, S.310, F.313 Chain F: S.47, R.49, I.79, A.80 15 PLIP interactions: 7 interactions with chain B, 6 interactions with chain A, 2 interactions with chain F Hydrogen bonds: B:Q.135, B:D.143, B:N.144, B:N.144, B:V.309, B:S.310, B:S.310, A:K.100, A:K.100, A:D.101, A:S.103, A:R.104, A:R.104, F:R.49 pi-Cation interactions: F:R.49 GDP.4: 18 residues within 4Å: Chain A: Q.135, V.142, D.143, N.144, Y.146, S.308, V.309, S.310, F.313 Chain B: K.100, D.101, K.102, S.103, R.104 Chain C: S.47, R.49, I.79, A.80 14 PLIP interactions: 3 interactions with chain B, 8 interactions with chain A, 3 interactions with chain C Hydrogen bonds: B:K.100, B:K.100, B:R.104, A:Q.135, A:D.143, A:N.144, A:Y.146, A:Y.146, A:V.309, A:S.310, C:R.49 Water bridges: A:N.144 pi-Cation interactions: C:R.49, C:R.49 GDP.12: 10 residues within 4Å: Chain B: R.49, A.80 Chain C: K.100, S.103, R.104 Chain D: D.143, N.144, L.145, Y.146, R.302 9 PLIP interactions: 4 interactions with chain D, 2 interactions with chain B, 3 interactions with chain C Hydrogen bonds: D:Q.135, D:N.144, D:N.144, D:Y.146, B:R.49, B:R.49, C:K.100, C:K.100, C:R.104 GDP.13: 16 residues within 4Å: Chain C: Q.135, D.143, N.144, S.308, V.309, S.310, F.313 Chain D: K.100, D.101, K.102, S.103, R.104 Chain E: S.47, R.49, I.79, A.80 15 PLIP interactions: 7 interactions with chain C, 2 interactions with chain E, 6 interactions with chain D Hydrogen bonds: C:Q.135, C:D.143, C:N.144, C:V.309, C:S.310, C:S.310, C:S.310, E:R.49, D:K.100, D:K.100, D:K.100, D:D.101, D:R.104, D:R.104 pi-Cation interactions: E:R.49 GDP.20: 16 residues within 4Å: Chain A: S.47, R.49, I.79, A.80 Chain E: Q.135, D.143, Y.146, S.308, V.309, S.310, F.313 Chain F: K.100, D.101, K.102, S.103, R.104 13 PLIP interactions: 6 interactions with chain E, 5 interactions with chain F, 2 interactions with chain A Hydrogen bonds: E:Q.135, E:D.143, E:N.144, E:Y.146, E:V.309, E:S.310, F:K.100, F:K.100, F:K.100, F:R.104, F:R.104, A:R.49 pi-Cation interactions: A:R.49 GDP.21: 15 residues within 4Å: Chain D: S.47, R.49, I.79, A.80 Chain E: K.100, D.101, K.102, S.103, R.104 Chain F: D.143, N.144, S.308, V.309, S.310, F.313 9 PLIP interactions: 4 interactions with chain E, 3 interactions with chain F, 2 interactions with chain D Hydrogen bonds: E:K.100, E:K.100, E:R.104, E:R.104, F:N.144, F:V.309, F:S.310 pi-Cation interactions: D:R.49, D:R.49

6 x PO4: PHOSPHATE ION

PO4.6: 10 residues within 4Å: Chain A: C.91, F.92, P.93, Y.94, A.95, R.96, M.222, I.252 Chain F: N.37, E.39 6 PLIP interactions: 1 interactions with chain F, 5 interactions with chain A Hydrogen bonds: F:N.37, A:F.92, A:Y.94, A:A.95, A:R.96 Salt bridges: A:R.96 PO4.9: 9 residues within 4Å: Chain B: C.91, F.92, P.93, Y.94, A.95, R.96, M.222, I.252 Chain C: E.39 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:A.95, B:R.96, C:E.39, C:E.39 Salt bridges: B:R.96 PO4.14: 9 residues within 4Å: Chain B: E.39 Chain C: C.91, F.92, P.93, Y.94, A.95, R.96, M.222, I.252 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:F.92, C:F.92, C:A.95 Salt bridges: C:R.96 PO4.16: 10 residues within 4Å: Chain D: C.91, F.92, P.93, Y.94, A.95, R.96, M.222, I.252 Chain E: N.37, E.39 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:Y.94, D:A.95, E:N.37, E:E.39, E:E.39 Salt bridges: D:R.96 PO4.17: 5 residues within 4Å: Chain D: D.224, T.225, C.226, G.227, T.228 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:D.224, D:T.225, D:C.226, D:G.227, D:T.228, D:T.228 PO4.23: 9 residues within 4Å: Chain A: E.39 Chain F: C.91, F.92, P.93, Y.94, A.95, R.96, M.222, I.252 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:A.95, F:R.96, A:N.37, A:E.39 Salt bridges: F:R.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, L. et al., PRPS2 enhances RNA m 6 A methylation by stimulating SAM synthesis through enzyme-dependent and independent mechanisms. Nat Commun (2025)

Release Date

2025-03-19

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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