SMTL ID : 8ypy.1

Crystal strcuture of human phosphoribosyl pyrophosphate synthetase2 (PRPS2) in complex with ligands

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.74 Å

Oligo State

homo-hexamer

Ligands

6 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)(Covalent)

APC.1: 10 residues within 4Å: Chain A: R.96, Q.97, D.98, H.133 Chain B: K.179 Chain F: F.35, N.37, E.39 Ligands: HSX.2, CD.3 15 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B, 5 interactions with chain F Hydrogen bonds: A:Q.97, A:Q.97, A:D.98, A:D.98, A:H.133, B:K.179, B:K.179, F:N.37, F:N.37, F:E.39 Salt bridges: A:H.133, B:K.179 pi-Cation interactions: A:R.96 pi-Stacking: F:F.35, F:F.35 APC.4: 11 residues within 4Å: Chain A: F.35, N.37, E.39 Chain E: K.179 Chain F: R.96, Q.97, D.98, K.99, K.100, H.133 Ligands: CD.22 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain F Hydrogen bonds: A:N.37, A:E.39, F:R.96, F:R.96, F:Q.97, F:D.98, F:K.99 pi-Stacking: A:F.35, A:F.35 Salt bridges: F:H.133 pi-Cation interactions: F:R.96 APC.10: 8 residues within 4Å: Chain B: R.96, Q.97, H.133 Chain C: F.35, N.37, E.39 Ligands: HSX.8, CD.9 10 PLIP interactions: 5 interactions with chain B, 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:Q.97, B:Q.97, C:N.37, C:N.37 Salt bridges: B:H.133, A:K.179 pi-Cation interactions: B:R.96, B:R.96 pi-Stacking: C:F.35, C:F.35 APC.11: 11 residues within 4Å: Chain B: F.35, N.37, E.39 Chain C: R.96, Q.97, D.98, H.133, D.174, G.176 Chain D: K.179 Ligands: CD.13 6 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: C:R.96, C:G.176, B:N.37 Salt bridges: C:H.133, D:K.179 pi-Cation interactions: C:R.96 APC.14: 12 residues within 4Å: Chain D: R.96, Q.97, D.98, K.100, H.133, D.174, G.176, D.227 Chain E: F.35, N.37, E.39 Ligands: CD.16 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:R.96, D:Q.97, D:D.98, D:D.98, D:H.133, E:E.39 Salt bridges: D:H.133 pi-Stacking: E:F.35, E:F.35 APC.18: 12 residues within 4Å: Chain D: F.35, N.37, E.39 Chain E: R.96, Q.97, D.98, K.99, H.133, D.174, G.176 Chain F: K.179 Ligands: CD.20 12 PLIP interactions: 7 interactions with chain E, 4 interactions with chain D, 1 interactions with chain F Hydrogen bonds: E:R.96, E:R.96, E:D.98, E:K.99, E:D.174, D:N.37, D:E.39 Salt bridges: E:H.133, F:K.179 pi-Cation interactions: E:R.96 pi-Stacking: D:F.35, D:F.35

6 x HSX: 5-O-phosphono-alpha-D-ribofuranose(Non-covalent)

HSX.2: 6 residues within 4Å: Chain A: T.228, C.229, G.230, T.231, R.263 Ligands: APC.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.227, A:T.228, A:T.228, A:C.229, A:G.230, A:T.231, A:T.231 Water bridges: A:M.225 Salt bridges: A:R.263 HSX.8: 7 residues within 4Å: Chain B: D.227, T.228, C.229, G.230, T.231, R.263 Ligands: APC.10 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.227, B:T.228, B:T.228, B:C.229, B:G.230, B:T.231, B:T.231 Salt bridges: B:K.197, B:R.263 HSX.12: 5 residues within 4Å: Chain C: T.228, C.229, G.230, T.231, R.263 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:T.228, C:T.228, C:C.229, C:G.230, C:T.231, C:T.231, C:R.263 Salt bridges: C:R.263 HSX.15: 5 residues within 4Å: Chain D: T.228, C.229, G.230, T.231, R.263 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:T.228, D:T.228, D:T.228, D:C.229, D:G.230, D:T.231, D:T.231, D:R.263 Salt bridges: D:R.263 HSX.19: 6 residues within 4Å: Chain E: R.96, D.227, T.228, C.229, G.230, T.231 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:D.227, E:T.228, E:T.228, E:C.229, E:G.230, E:T.231 Salt bridges: E:R.96, E:K.197 HSX.21: 5 residues within 4Å: Chain F: T.228, C.229, G.230, T.231, R.263 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:C.229, F:G.230, F:T.231, F:T.231 Salt bridges: F:R.263

6 x CD: CADMIUM ION(Non-covalent)

CD.3: 3 residues within 4Å: Chain A: D.174, D.223 Ligands: APC.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.223 CD.9: 3 residues within 4Å: Chain B: D.174, D.223 Ligands: APC.10 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.174 CD.13: 3 residues within 4Å: Chain C: D.174, D.223 Ligands: APC.11 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.174, C:D.174, C:D.223 CD.16: 2 residues within 4Å: Chain D: D.223 Ligands: APC.14 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.223 CD.20: 3 residues within 4Å: Chain E: D.174, D.223 Ligands: APC.18 No protein-ligand interaction detected (PLIP) CD.22: 3 residues within 4Å: Chain F: D.174, D.223 Ligands: APC.4 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.174

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

PO4.5: 6 residues within 4Å: Chain A: D.131, E.151, V.154, R.180, I.184, T.252 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.252, A:T.252 Salt bridges: A:R.180 PO4.6: 3 residues within 4Å: Chain A: Y.149, E.151, S.183 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.183 PO4.7: 9 residues within 4Å: Chain A: F.92, P.93, Y.94, A.95, R.96, M.225, I.255 Chain F: N.37, E.39 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:Y.94, A:A.95, A:R.96, F:N.37, F:E.39 Salt bridges: A:R.96 PO4.17: 9 residues within 4Å: Chain D: F.92, P.93, Y.94, A.95, R.96, M.225, I.255 Chain E: N.37, E.39 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:Y.94, D:A.95, D:R.96, E:N.37, E:E.39 Salt bridges: D:R.96 PO4.23: 8 residues within 4Å: Chain A: N.37, E.39 Chain F: C.91, F.92, P.93, Y.94, A.95, R.96 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:Y.94, F:A.95, F:R.96, F:R.96, A:N.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, L. et al., Crystal strcuture of human phosphoribosyl pyrophosphate synthetase2 (PRPS2) in complex with ligands. To Be Published

Release Date

2025-03-19

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