SMTL ID : 5i1f.1

Crystal structure of UTP-glucose-1-phosphate uridylyltransferase from Burkholderia vietnamiensis in complex with Uridine-5'-diphosphate-glucose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

2 x UPG: URIDINE-5'-DIPHOSPHATE-GLUCOSE(Non-covalent)

UPG.1: 27 residues within 4Å: Chain A: P.18, V.19, A.20, G.21, K.35, E.36, Q.113, A.116, L.117, G.118, L.119, A.122, L.139, D.141, D.142, Y.179, G.180, E.199, K.200, V.212, V.213, G.214, Q.238, T.240, R.261 Ligands: MG.2, MG.3 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:A.20, A:G.21, A:E.36, A:E.36, A:Q.113, A:Q.113, A:G.118, A:D.142, A:G.180, A:E.199, A:V.212, A:G.214, A:T.240, A:R.261 Water bridges: A:V.19, A:G.21, A:K.35, A:A.140, A:K.200, A:K.200, A:K.200, A:K.200 Salt bridges: A:K.35, A:K.200, A:K.200 UPG.10: 27 residues within 4Å: Chain B: P.18, V.19, A.20, G.21, K.35, E.36, Q.113, A.116, L.117, G.118, L.119, A.122, L.139, D.141, D.142, Y.179, G.180, E.199, K.200, V.212, V.213, G.214, Q.238, T.240, R.261 Ligands: MG.11, MG.12 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:A.20, B:G.21, B:E.36, B:Q.113, B:Q.113, B:G.118, B:D.142, B:G.180, B:E.199, B:V.212, B:G.214, B:R.261 Water bridges: B:V.19, B:G.21, B:K.35, B:A.140, B:K.200, B:K.200, B:K.200, B:K.200, B:Y.216, B:T.240 Salt bridges: B:K.35, B:K.200, B:K.200

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: E.236 Ligands: UPG.1 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain A: K.35, D.141 Ligands: UPG.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.141, H2O.1, H2O.3, H2O.5 MG.11: 2 residues within 4Å: Chain B: E.236 Ligands: UPG.10 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain B: K.35, D.141 Ligands: UPG.10 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.141, H2O.8, H2O.10, H2O.11

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: A.172, P.173, A.174 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: P.134, F.158, K.219 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: K.219, P.220, K.221 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: F.262, D.263, G.269 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: G.21, L.22, G.23, K.35 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: R.25, S.266, K.267 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: A.172, P.173, A.174 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: P.134, F.158, K.219 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain B: K.219, P.220, K.221 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain B: F.262, D.263, G.269 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain B: G.21, L.22, G.23, K.35 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain B: R.25, S.266, K.267 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal structure of UTP-glucose-1-phosphate uridylyltransferase from Burkholderia vietnamiensis in complex with Uridine-5'-diphosphate-glucose. to be published

Release Date

2016-03-02

Peptides

UTP--glucose-1-phosphate uridylyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

UTP--glucose-1-phosphate uridylyltransferase