SMTL ID : 5t3o.1

Crystal structure of the Phosphorybosylpyrophosphate synthetase II from Thermus thermophilus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

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

ADP.1: 12 residues within 4Å: Chain A: S.91, Y.92, R.94, S.95, K.97, D.99, H.128, D.168, R.193 Chain F: F.33, N.35, N.37 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain F Hydrogen bonds: A:S.95, A:S.95, A:D.99, A:D.168, A:R.193, F:N.35, F:N.37 Salt bridges: A:K.97, A:K.97, A:H.128, A:R.193 pi-Stacking: F:F.33 ADP.4: 12 residues within 4Å: Chain B: S.91, Y.92, R.94, S.95, K.97, D.99, H.128, D.168, R.193 Chain E: F.33, N.35, N.37 11 PLIP interactions: 3 interactions with chain E, 8 interactions with chain B Hydrogen bonds: E:N.35, E:N.37, B:R.94, B:S.95, B:S.95, B:D.99 pi-Stacking: E:F.33 Salt bridges: B:K.97, B:K.97, B:H.128, B:K.191 ADP.7: 10 residues within 4Å: Chain C: S.91, Y.92, R.94, S.95, K.97, D.99, H.128 Chain D: F.33, N.35, N.37 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:N.35, D:N.37, C:S.95, C:S.95 pi-Stacking: D:F.33 Salt bridges: C:K.97, C:K.97, C:H.128 ADP.10: 12 residues within 4Å: Chain C: F.33, N.35, N.37 Chain D: S.91, Y.92, R.94, S.95, K.97, D.99, H.128, D.168, R.193 12 PLIP interactions: 9 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:S.95, D:S.95, D:D.99, D:D.168, D:R.193, C:N.35, C:N.37 Salt bridges: D:K.97, D:K.97, D:H.128, D:R.193 pi-Stacking: C:F.33 ADP.13: 12 residues within 4Å: Chain B: F.33, N.35, N.37 Chain E: S.91, Y.92, R.94, S.95, K.97, D.99, H.128, D.168, R.193 11 PLIP interactions: 8 interactions with chain E, 3 interactions with chain B Hydrogen bonds: E:R.94, E:S.95, E:S.95, E:D.99, B:N.35, B:N.37 Salt bridges: E:K.97, E:K.97, E:H.128, E:K.191 pi-Stacking: B:F.33 ADP.16: 10 residues within 4Å: Chain A: F.33, N.35, N.37 Chain F: S.91, Y.92, R.94, S.95, K.97, D.99, H.128 8 PLIP interactions: 5 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:S.95, F:S.95, A:N.35, A:N.37 Salt bridges: F:K.97, F:K.97, F:H.128 pi-Stacking: A:F.33

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: R.102 Chain D: S.301, V.302, S.303 Chain F: S.45, R.47 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A, 2 interactions with chain F Hydrogen bonds: D:V.302, D:S.303 Salt bridges: A:R.102, F:R.47 Water bridges: F:R.47 SO4.3: 7 residues within 4Å: Chain A: V.194, I.220, S.221, T.222, A.223, G.224, S.225 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.221, A:T.222, A:T.222, A:T.222, A:A.223, A:G.224, A:S.225 SO4.5: 6 residues within 4Å: Chain A: S.45, R.47 Chain B: S.301, V.302, S.303 Chain F: R.102 7 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B, 1 interactions with chain F Hydrogen bonds: A:S.45, B:S.301, B:V.302, B:S.303 Water bridges: A:R.47 Salt bridges: A:R.47, F:R.102 SO4.6: 8 residues within 4Å: Chain B: R.193, D.196, I.220, S.221, T.222, A.223, G.224, S.225 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:S.221, B:T.222, B:A.223, B:G.224, B:S.225 Water bridges: B:R.94, B:R.94, B:R.193, B:R.193, B:A.223, B:L.226 Salt bridges: B:R.193 SO4.8: 6 residues within 4Å: Chain B: S.45, R.47 Chain C: S.301, V.302, S.303 Chain E: R.102 7 PLIP interactions: 4 interactions with chain B, 1 interactions with chain E, 2 interactions with chain C Hydrogen bonds: B:S.45, C:V.302, C:S.303 Water bridges: B:L.46, B:R.47 Salt bridges: B:R.47, E:R.102 SO4.9: 6 residues within 4Å: Chain C: I.220, S.221, T.222, A.223, G.224, S.225 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:S.221, C:T.222, C:A.223, C:G.224, C:S.225 Water bridges: C:R.94, C:R.94, C:A.223, C:L.226 SO4.11: 6 residues within 4Å: Chain A: S.301, V.302, S.303 Chain C: S.45, R.47 Chain D: R.102 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A, 1 interactions with chain D Water bridges: C:R.47 Salt bridges: C:R.47, D:R.102 Hydrogen bonds: A:V.302, A:S.303 SO4.12: 7 residues within 4Å: Chain D: V.194, I.220, S.221, T.222, A.223, G.224, S.225 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.221, D:T.222, D:T.222, D:A.223, D:G.224, D:S.225 SO4.14: 6 residues within 4Å: Chain C: R.102 Chain D: S.45, R.47 Chain E: S.301, V.302, S.303 7 PLIP interactions: 3 interactions with chain E, 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: E:S.301, E:V.302, E:S.303, D:S.45 Water bridges: D:R.47 Salt bridges: D:R.47, C:R.102 SO4.15: 8 residues within 4Å: Chain E: R.193, D.196, I.220, S.221, T.222, A.223, G.224, S.225 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:S.221, E:T.222, E:A.223, E:G.224, E:S.225 Water bridges: E:R.94, E:R.94, E:R.193, E:T.222, E:A.223, E:L.226 Salt bridges: E:R.193 SO4.17: 6 residues within 4Å: Chain B: R.102 Chain E: S.45, R.47 Chain F: S.301, V.302, S.303 7 PLIP interactions: 4 interactions with chain E, 2 interactions with chain F, 1 interactions with chain B Hydrogen bonds: E:S.45, F:V.302, F:S.303 Water bridges: E:L.46, E:R.47 Salt bridges: E:R.47, B:R.102 SO4.18: 6 residues within 4Å: Chain F: I.220, S.221, T.222, A.223, G.224, S.225 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:S.221, F:T.222, F:A.223, F:G.224, F:S.225 Water bridges: F:R.94, F:R.94, F:A.223, F:L.226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Timofeev, V.I. et al., Crystal structure of recombinant phosphoribosylpyrophosphate synthetase 2 from Thermus thermophilus HB27 complexed with ADP and sulfate ions. Acta Crystallogr F Struct Biol Commun (2017)

Release Date

2017-06-14

Peptides

Ribose-phosphate pyrophosphokinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Ribose-phosphate pyrophosphokinase