SMTL ID : 3g6w.1

Asymetric GTP bound structure of UPRTase from Sulfolobus solfataricus containing PRPP-mg2+ in half of the active sites and R5P and PPi in the other half

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

4 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 12 residues within 4Å: Chain A: K.30, R.34, R.37 Chain B: R.37, K.91, P.94 Chain D: I.26, N.27, K.30, R.34 Ligands: MG.2, GTP.12 18 PLIP interactions: 8 interactions with chain A, 4 interactions with chain B, 6 interactions with chain D Water bridges: A:K.30, A:R.34, A:K.91 Salt bridges: A:K.30, A:K.30, A:R.34, A:R.37, A:R.37, B:R.37, B:K.91, B:K.91, D:K.30 Hydrogen bonds: B:K.91, D:N.27, D:N.27, D:N.27, D:R.34, D:R.34 GTP.5: 11 residues within 4Å: Chain A: K.91, P.94 Chain B: K.30, R.34, R.37 Chain C: I.26, N.27, K.30, R.34 Ligands: MG.6, GTP.11 12 PLIP interactions: 4 interactions with chain C, 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: C:N.27, C:R.34, C:R.34, A:K.91 Salt bridges: C:K.30, B:K.30, B:K.30, B:R.34, B:R.37, B:R.37, A:K.91, A:K.91 GTP.11: 11 residues within 4Å: Chain B: I.26, N.27, K.30, R.34 Chain C: K.30, R.34 Chain D: R.37, K.91, P.94 Ligands: GTP.5, MG.6 13 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C, 6 interactions with chain B Hydrogen bonds: D:K.91, B:N.27, B:N.27, B:N.27, B:R.34, B:R.34 Salt bridges: D:R.37, D:R.37, D:K.91, D:K.91, C:K.30, C:R.34, B:K.30 GTP.12: 11 residues within 4Å: Chain A: I.26, N.27, K.30, R.34 Chain C: R.37, K.91, P.94 Chain D: K.30, R.34 Ligands: GTP.1, MG.2 17 PLIP interactions: 10 interactions with chain A, 4 interactions with chain C, 3 interactions with chain D Hydrogen bonds: A:N.27, A:N.27, A:N.27, A:R.34, A:R.34 Water bridges: A:K.30, A:K.30, A:K.30, A:K.91 Salt bridges: A:K.30, C:R.37, C:R.37, C:K.91, C:K.91, D:K.30, D:K.30, D:R.34

4 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2: 2 residues within 4Å: Ligands: GTP.1, GTP.12 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain A: L.79, R.80, A.81 Ligands: PRP.3 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Ligands: GTP.5, GTP.11 No protein-ligand interaction detected (PLIP) MG.15: 4 residues within 4Å: Chain D: L.79, R.80, A.81 Ligands: PRP.13 No protein-ligand interaction detected (PLIP)

2 x PRP: 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose(Non-covalent)

PRP.3: 15 residues within 4Å: Chain A: R.80, A.81, R.105, M.117, D.140, M.142, I.143, A.144, T.145, A.146, S.147, T.148, D.209, G.211 Ligands: MG.4 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.105, A:D.140, A:A.144, A:T.145, A:A.146, A:S.147, A:T.148, A:T.148, A:G.211 Water bridges: A:A.81, A:A.81, A:A.146, A:M.149 Salt bridges: A:R.80, A:R.105, A:R.105, C:K.125 PRP.13: 17 residues within 4Å: Chain B: K.125 Chain D: L.79, R.80, A.81, A.103, S.104, R.105, D.140, M.142, I.143, A.144, T.145, A.146, S.147, T.148 Ligands: HSX.14, MG.15 14 PLIP interactions: 13 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:L.79, D:A.81, D:R.105, D:D.140, D:A.144, D:T.145, D:A.146, D:S.147, D:T.148, D:T.148 Water bridges: D:M.149 Salt bridges: D:R.80, D:R.105, B:K.125

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

HSX.7: 10 residues within 4Å: Chain B: R.105, D.140, M.142, I.143, A.144, T.145, A.146, S.147, T.148 Ligands: POP.8 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:D.140, B:A.144, B:T.145, B:A.146, B:S.147, B:T.148, B:T.148 Water bridges: B:M.149 Salt bridges: B:R.105, B:R.105 HSX.9: 12 residues within 4Å: Chain C: I.78, A.81, R.105, D.140, M.142, I.143, A.144, T.145, A.146, S.147, T.148 Ligands: POP.10 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:D.140, C:A.144, C:T.145, C:A.146, C:S.147, C:T.148, C:T.148 Salt bridges: C:R.105 HSX.14: 8 residues within 4Å: Chain C: L.58 Chain D: E.107, M.142, Y.202, I.203, G.208, D.209 Ligands: PRP.13 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.107, D:E.107, D:Y.202, D:I.203

2 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.8: 7 residues within 4Å: Chain B: L.79, R.80, A.81, D.209, G.211 Chain D: Y.123 Ligands: HSX.7 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:Y.123, D:Y.123, B:A.81 Salt bridges: B:R.80 POP.10: 7 residues within 4Å: Chain A: Y.123, K.125 Chain C: L.79, R.80, A.81, A.103 Ligands: HSX.9 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:A.81, C:A.103, A:Y.123 Salt bridges: C:R.80, A:K.125, A:K.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Christoffersen, S. et al., Structural and kinetic studies of the allosteric transition in Sulfolobus solfataricus uracil phosphoribosyltransferase: Permanent activation by engineering of the C-terminus. J.Mol.Biol. (2009)

Release Date

2009-09-01

Peptides

Uracil phosphoribosyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Uracil phosphoribosyltransferase

Related Entries With Identical Sequence