SMTL ID : 1o5o.1

Crystal structure of Uracil phosphoribosyltransferase (TM0721) from Thermotoga maritima at 2.30 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: L.90, R.91, A.92, I.114 Chain D: Y.127 Ligands: U5P.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.90, A:R.91, A:A.92 Water bridges: A:G.214 Salt bridges: A:R.91 SO4.2: 4 residues within 4Å: Chain A: R.199, N.201, D.202, I.207 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.200, A:D.202 Salt bridges: A:R.199 SO4.3: 4 residues within 4Å: Chain A: G.37, P.38, R.219 Chain D: K.82 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Water bridges: A:R.219 Salt bridges: A:R.219, D:K.82 SO4.5: 8 residues within 4Å: Chain B: L.90, R.91, A.92, D.212, G.214 Chain C: Y.127, K.129 Ligands: U5P.7 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:R.91, B:A.92, C:Y.127 Water bridges: B:G.214 Salt bridges: B:R.91, C:K.129 SO4.6: 3 residues within 4Å: Chain B: R.199, N.201, D.202 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.202 Salt bridges: B:R.199 SO4.8: 6 residues within 4Å: Chain B: Y.127 Chain C: L.90, R.91, A.92, I.114 Ligands: U5P.9 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:L.90, C:R.91, C:A.92, B:Y.127 Water bridges: C:G.214, C:G.214 Salt bridges: C:R.91 SO4.10: 5 residues within 4Å: Chain A: Y.127 Chain D: R.91, A.92, G.214 Ligands: U5P.13 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:R.91, D:A.92 Water bridges: D:G.214, D:G.214 Salt bridges: D:R.91, A:K.129 SO4.11: 3 residues within 4Å: Chain D: R.199, N.201, D.202 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.202, D:D.202 Water bridges: D:H.203 Salt bridges: D:R.199 SO4.12: 4 residues within 4Å: Chain A: K.82 Chain D: G.37, P.38, R.219 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Salt bridges: A:K.82, D:R.219 Water bridges: D:R.219

4 x U5P: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U5P.4: 16 residues within 4Å: Chain A: R.116, D.143, M.145, L.146, A.147, T.148, G.149, V.150, S.151, G.204, Y.205, I.206, G.211, D.212, A.213 Ligands: SO4.1 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:A.147 Hydrogen bonds: A:A.147, A:T.148, A:G.149, A:V.150, A:S.151, A:S.151, A:I.206, A:G.211, A:A.213 Water bridges: A:R.116, A:D.143, A:D.143, A:M.145, A:S.152, A:L.210, A:G.214, A:G.214 Salt bridges: A:R.116 pi-Stacking: A:Y.205 U5P.7: 16 residues within 4Å: Chain B: R.116, D.143, M.145, L.146, A.147, T.148, G.149, V.150, S.151, G.204, Y.205, I.206, G.211, D.212, A.213 Ligands: SO4.5 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:A.147 Hydrogen bonds: B:D.143, B:A.147, B:T.148, B:G.149, B:V.150, B:S.151, B:S.151, B:S.151, B:I.206, B:G.211, B:A.213 Water bridges: B:S.152, B:G.214, B:G.214 Salt bridges: B:R.116 pi-Stacking: B:Y.205 U5P.9: 16 residues within 4Å: Chain C: R.116, D.143, M.145, L.146, A.147, T.148, G.149, V.150, S.151, G.204, Y.205, I.206, G.211, D.212, A.213 Ligands: SO4.8 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:A.147 Hydrogen bonds: C:A.147, C:T.148, C:G.149, C:S.151, C:S.151, C:I.206, C:G.211, C:A.213 Water bridges: C:R.91, C:R.116, C:R.116, C:S.152, C:G.214, C:G.214 Salt bridges: C:R.116 pi-Stacking: C:Y.205 U5P.13: 15 residues within 4Å: Chain D: R.116, D.143, M.145, A.147, T.148, G.149, V.150, S.151, G.204, Y.205, I.206, G.211, D.212, A.213 Ligands: SO4.10 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:A.147 Hydrogen bonds: D:R.116, D:D.143, D:A.147, D:T.148, D:G.149, D:V.150, D:S.151, D:S.151, D:S.151, D:I.206, D:G.211, D:A.213 Water bridges: D:S.152, D:G.214, D:G.214 Salt bridges: D:R.116 pi-Stacking: D:Y.205

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of Uracil phosphoribosyltransferase (TM0721) from Thermotoga maritima at 2.30 A resolution. To be published

Release Date

2003-10-14

Peptides

Uracil phosphoribosyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Uracil phosphoribosyltransferase